3-111482938-T-G

Variant names:

• chr3-111482938-T-G
• rs76884941
• ENST00000460744.1:c.-98-58997T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460744.1(CD96):​c.-98-58997T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,282 control chromosomes in the GnomAD database, including 253 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 0.050 (253 hom., cov: 32)
• Consequence: CD96 ENST00000460744.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 5 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: AD, Unknown, AR Classification: LIMITED Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics

ENSG00000239311 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0676 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD96	ENST00000460744.1	TSL:4	c.-98-58997T>G		intron	N/A	ENSP00000475194.1	U3KPT0
	ENSG00000239311	ENST00000497896.1	TSL:3	n.208+13950A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7596 AN: 152164 Hom.: 253 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.00924

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0499 AC: 7592 AN: 152282 Hom.: 253 Cov.: 32 AF XY: 0.0517 AC XY: 3848 AN XY: 74452

African (AFR) AF: 0.0167 AC: 694 AN: 41552

American (AMR) AF: 0.0325 AC: 498 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3472

East Asian (EAS) AF: 0.00907 AC: 47 AN: 5184

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4822

European-Finnish (FIN) AF: 0.110 AC: 1170 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0693 AC: 4712 AN: 68018

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0570 Hom.: 579

Bravo AF: 0.0440

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.54
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs76884941; hg19: chr3-111201785;