Is INTS1 p.Ile510= (c.1530C>T) pathogenic?

INTS1 p.Ile510= (c.1530C>T) is classified Likely benign in INTS1 (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with INTS1 p.Ile510= (c.1530C>T)?

INTS1 p.Ile510= (c.1530C>T) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is INTS1 p.Ile510= (c.1530C>T) in the general population?

INTS1 p.Ile510= (c.1530C>T) is absent from gnomAD v4.1 (gnomAD).

INTS1 p.Ile510=

c.1530C>T · rs1188419101 · VCV2681332

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4.3	GERP 1.6, phastCons 1
Overall
CADD	11.43	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: INTS1
Protein: p.Ile510=
Coding: c.1530C>T
MANE Select: NM_001080453
dbSNP: rs1188419101
Type: single nucleotide variant
Location: chr7:1497210 (GRCh38)
Gene constraint: LOEUF 0.785 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.49 · 8 PDB

Full INTS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

INTS1 c.3156+8C>T Conflicting classifications of pathogenicity ★ same condition
INTS1 c.3850+76G>A Uncertain significance ★ same condition
INTS1 p.Gly73Ser Uncertain significance ⚠ same condition
INTS1 p.Lys435Asn Uncertain significance ⚠ same condition
INTS1 p.Met888Val Uncertain significance ⚠ same condition
INTS1 c.1138-4G>A Likely benign same condition
INTS1 c.2646+10G>A Likely benign same condition
INTS1 p.Ala1234= Likely benign 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/ints1-p-ile510 (accessed [today's date]).

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