rs7624812

Positions:

• chr3-111335835-C-T

Variant summary

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

The ENST00000460744.1(CD96):​c.-325-28678C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,076 control chromosomes in the GnomAD database, including 4,402 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 0.23 (4402 hom., cov: 32)
• Consequence: CD96 ENST00000460744.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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.-325-28678C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34997 AN: 151958 Hom.: 4403 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.230 AC: 35011 AN: 152076 Hom.: 4402 Cov.: 32 AF XY: 0.236 AC XY: 17524 AN XY: 74330

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.238

Alfa AF: 0.194 Hom.: 1710

Bravo AF: 0.229

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7624812; hg19: chr3-111054682;