Is CD48 p.Thr233= (c.699G>A) pathogenic?

CD48 p.Thr233= (c.699G>A) is classified Benign/Likely benign in CD48 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-11-17). Rare (popmax 0.987%, nfe).

How common is CD48 p.Thr233= (c.699G>A) in the general population?

CD48 p.Thr233= (c.699G>A) is rare (popmax 0.987%, nfe) (gnomAD).

CD48 p.Thr233=

c.699G>A · rs150535390 · VCV2639504

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.987%, nfe)

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 -2.6	GERP -2.7
Overall
CADD	1.081	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.987% European (non-Finnish) · 11,647/1,179,906 alleles

Filtering AF 0.972% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.966%

Overall 0.87% 14,045/1,614,002 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	3.06%	33
European (non-Finnish)grpmax	0.987%	101
Remaining individualsnot grpmax-eligible	0.958%	104
Admixed American	0.81%	123
Middle Eastern	0.792%	126
African / African-American	0.259%	387
Amishnot grpmax-eligible	0.11%	912
South Asian	0.108%	929
Finnishnot grpmax-eligible	0.1%	1,000
East Asian	0.00223%	44,876

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CD48
Protein: p.Thr233=
Coding: c.699G>A
MANE Select: NM_001778
dbSNP: rs150535390
Type: single nucleotide variant
Location: chr1:160679085 (GRCh38)
Gene constraint: LOEUF 1.31 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.20 · 1 PDB

Full CD48 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD48 p.Thr216Ile Uncertain significance ★★ ⚠ same type
CD48 c.652+73G>T Benign ★★ same type
CD48 p.Gln90= Benign ★★ same type
CD48 p.Leu30= Benign ★★ same type
CD48 p.Ala93Thr Uncertain significance ★ ⚠ same type
CD48 p.Arg192Met Uncertain significance ★ ⚠ same type
CD48 p.Asn178Lys Uncertain significance ★ ⚠ same type
CD48 p.Asn44Ile 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/cd48-p-thr233 (accessed [today's date]).

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