rs7634000

Positions:

• chr3-111329503-T-C
• chr3-111329503-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460744.1(CD96):​c.-325-35010T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,078 control chromosomes in the GnomAD database, including 19,864 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (19864 hom., cov: 32)
• Consequence: CD96 ENST00000460744.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

Genes affected

CD96 (HGNC:16892): (CD96 molecule) The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membrane protein. The protein may play a role in the adhesive interactions of activated T and NK cells during the late phase of the immune response. It may also function in antigen presentation. Alternative splicing generates multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD96	ENST00000460744.1	c.-325-35010T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72403 AN: 151960 Hom.: 19858 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.482

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.476 AC: 72418 AN: 152078 Hom.: 19864 Cov.: 32 AF XY: 0.481 AC XY: 35778 AN XY: 74340

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.480

Alfa AF: 0.549 Hom.: 9995

Bravo AF: 0.462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7634000; hg19: chr3-111048350;