Is RINT1 p.Ile155= (c.465C>T) pathogenic?

RINT1 p.Ile155= (c.465C>T) is classified Benign in RINT1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-03). Low-frequency (popmax 4.74%, eas).

How common is RINT1 p.Ile155= (c.465C>T) in the general population?

RINT1 p.Ile155= (c.465C>T) is low-frequency (popmax 4.74%, eas) (gnomAD).

RINT1 p.Ile155=

c.465C>T · rs79893877 · VCV416394

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.74%, eas)

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 -6.4
Overall
CADD	6.307	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.74% East Asian · 2,127/44,884 alleles

Filtering AF 4.57% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.5%

Overall 0.486% 7,846/1,613,976 alleles · low-frequency exomes 6,887/1,461,774 · genomes 959/152,202 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	4.74%	21
Admixed American	2.6%	38
Finnishnot grpmax-eligible	2.14%	47
Remaining individualsnot grpmax-eligible	0.536%	187
African / African-American	0.355%	282
South Asian	0.246%	406
Middle Eastern	0.182%	551
European (non-Finnish)	0.166%	604
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,802

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: RINT1
Protein: p.Ile155=
Coding: c.465C>T
MANE Select: NM_021930
dbSNP: rs79893877
Type: single nucleotide variant
Location: chr7:105542599 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.97

Full RINT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RINT1 p.Ile155Leu Uncertain significance ★★ ⚠ same residue
RINT1 p.Ile155Met Uncertain significance ★★ ⚠ same residue
RINT1 p.Ile155Thr Uncertain significance ★ ⚠ same residue
RINT1 c.1107+1G>T Likely pathogenic ★★ same type
RINT1 c.1886+5G>A Uncertain significance ★★ same type
RINT1 c.516-3C>T Uncertain significance ★★ same type
RINT1 c.840-12T>A Uncertain significance ★★ same type
RINT1 c.840-3C>G 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/rint1-p-ile155 (accessed [today's date]).

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