3-111514392-C-A

Position:

• chr3-111514392-C-A

Variant summary

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

The XR_001740846.1(LOC105374039):​n.224-27543C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0495 in 152,282 control chromosomes in the GnomAD database, including 257 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 0.049 (257 hom., cov: 32)
• Consequence: LOC105374039 XR_001740846.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

LOC105374039 (HGNC:):

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374039	XR_001740846.1	n.224-27543C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD96	ENST00000460744.1	c.-98-27543C>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7537 AN: 152164 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0692

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0495 AC: 7533 AN: 152282 Hom.: 257 Cov.: 32 AF XY: 0.0514 AC XY: 3829 AN XY: 74448

Gnomad4 AFR AF: 0.0154

Gnomad4 AMR AF: 0.0326

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.00906

Gnomad4 SAS AF: 0.0472

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0692

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0595 Hom.: 400

Bravo AF: 0.0435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.056
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56238310; hg19: chr3-111233239;