chr3-111335835-C-T

Variant names:

• chr3-111335835-C-T
• rs7624812
• ENST00000460744.1:c.-325-28678C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

CD96 Gene-Disease associations (from GenCC):

• C syndrome

  Inheritance: Unknown, AD, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460744.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD96	ENST00000460744.1	TSL:4	c.-325-28678C>T		intron	N/A	ENSP00000475194.1

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

African (AFR) AF: 0.305 AC: 12652 AN: 41474

American (AMR) AF: 0.176 AC: 2688 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 626 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1841 AN: 5156

South Asian (SAS) AF: 0.271 AC: 1307 AN: 4826

European-Finnish (FIN) AF: 0.270 AC: 2852 AN: 10550

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12358 AN: 68006

Other (OTH) AF: 0.238 AC: 501 AN: 2104

Alfa AF: 0.195 Hom.: 1891

Bravo AF: 0.229

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.37
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7624812; hg19: chr3-111054682;