rs7643682

Positions:

• chr3-111547729-C-T

Variant summary

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

The NM_005816.5(CD96):​c.418+2327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 152,134 control chromosomes in the GnomAD database, including 1,444 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 0.081 (1444 hom., cov: 32)
• Consequence: CD96 NM_005816.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD96	NM_005816.5	c.418+2327C>T		intron_variant		ENST00000352690.9	NP_005807.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD96	ENST00000352690.9	c.418+2327C>T		intron_variant		1	NM_005816.5	ENSP00000342040	P2

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12355 AN: 152016 Hom.: 1440 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.00632

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0814 AC: 12386 AN: 152134 Hom.: 1444 Cov.: 32 AF XY: 0.0788 AC XY: 5864 AN XY: 74374

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.0316

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.00632

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0518 Hom.: 108

Bravo AF: 0.0914

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7643682; hg19: chr3-111266576;