Is INMT p.Ser84= (c.252C>T) pathogenic?

INMT p.Ser84= (c.252C>T) is classified Benign in INMT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-15). Rare (popmax 0.429%, afr).

How common is INMT p.Ser84= (c.252C>T) in the general population?

INMT p.Ser84= (c.252C>T) is rare (popmax 0.429%, afr) (gnomAD).

INMT p.Ser84=

c.252C>T · rs141846285 · VCV729936

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.429%, afr)

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 -7.4	GERP -3.8
Overall
CADD	1.032	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.429% African / African-American · 322/75,060 alleles

Filtering AF 0.39% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.375%

Overall 0.0249% 402/1,614,196 alleles · rare exomes 195/1,461,890 · genomes 207/152,306 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.429%	233
Admixed American	0.0716%	1,396
Remaining individualsnot grpmax-eligible	0.032%	3,125
Middle Eastern	0.0165%	6,062
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606
South Asian	0.0022%	45,542
European (non-Finnish)	0.0011%	90,771

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: INMT
Protein: p.Ser84=
Coding: c.252C>T
MANE Select: NM_006774
dbSNP: rs141846285
Type: single nucleotide variant
Location: chr7:30753828 (GRCh38)
Gene constraint: LOEUF 1.467 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.14 · 1 PDB
Residue 84: a β-strand

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

Similar variants

INMT c.363-7T>A Likely benign ★★ same type
INMT p.Ala104Thr Uncertain significance ★ ⚠ same type
INMT p.Ala134Glu Uncertain significance ★ ⚠ same type
INMT p.Ala215Thr Uncertain significance ★ ⚠ same type
INMT p.Ala247Ser Uncertain significance ★ ⚠ same type
INMT p.Ala247Val Uncertain significance ★ ⚠ same type
INMT p.Arg137Trp Uncertain significance ★ ⚠ same type
INMT p.Arg177His Uncertain significance ★ ⚠ same type

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/inmt-p-ser84 (accessed [today's date]).

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