Is TERT p.Arg962= (c.2886C>T) pathogenic?

TERT p.Arg962= (c.2886C>T) is classified Conflicting classifications of pathogenicity in TERT (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2026-01-12). Ultra-rare (popmax 0.0111%, eas); Associated with aplastic anemia.

How common is TERT p.Arg962= (c.2886C>T) in the general population?

TERT p.Arg962= (c.2886C>T) is ultra-rare (popmax 0.0111%, eas) (gnomAD).

TERT p.Arg962=

Q: What condition is associated with TERT p.Arg962= (c.2886C>T)?

TERT p.Arg962= (c.2886C>T) is associated with aplastic anemia, dyskeratosis congenita, autosomal dominant 2, pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 (ClinVar).

c.2886C>T · rs542440625 · VCV350593

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0111%, eas)

Conditions

aplastic anemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.4	GERP -2
Overall
CADD	7.543	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0111% East Asian · 5/44,886 alleles

Filtering AF 0.00514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00375%

Overall 0.00291% 47/1,614,186 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0111%	8,977
South Asian	0.00988%	10,120
African / African-American	0.00533%	18,763
Admixed American	0.00333%	30,017
European (non-Finnish)	0.0022%	45,385
Remaining individualsnot grpmax-eligible	0.0016%	62,510

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: TERT
Protein: p.Arg962=
Coding: c.2886C>T
MANE Select: NM_198253
dbSNP: rs542440625
Type: single nucleotide variant
Location: chr5:1260558 (GRCh38)
Gene constraint: LOEUF 0.593 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 80.98 · 32 PDB
Residue 962: the 'cte' region

Full TERT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

aplastic anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dyskeratosis congenita, autosomal dominant 2 pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1 dyskeratosis congenita idiopathic pulmonary fibrosis

Similar variants

TERT p.Arg962Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
TERT p.Arg962His Conflicting classifications of pathogenicity ★ ⚠ same residue
TERT p.Arg962Leu Uncertain significance ★ ⚠ same residue
TERT p.Arg962Pro Uncertain significance ★ ⚠ same residue
TERT p.Arg962Ser Uncertain significance ★ ⚠ same residue
TERT c.2130+1G>A Likely pathogenic ★★ same condition
TERT c.2130+2T>G Likely pathogenic ★★ same condition
TERT c.2131-2A>G Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tert-p-arg962 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown