Variant rs763362 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001303618.2(CD226):c.886-122T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 922,208 control chromosomes in the GnomAD database, including 73,085 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 0.37 ( 10624 hom., cov: 32)

Exomes 𝑓: 0.40 ( 62461 hom. )

Consequence

CD226
NM_001303618.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.788

Variant links:

Genes affected

CD226 (HGNC:16961): (CD226 molecule) This gene encodes a glycoprotein expressed on the surface of NK cells, platelets, monocytes and a subset of T cells. It is a member of the Ig-superfamily containing 2 Ig-like domains of the V-set. The protein mediates cellular adhesion of platelets and megakaryocytic cells to vascular endothelial cells. The protein also plays a role in megakaryocytic cell maturation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

CD226 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD226	NM_001303618.2 linkuse as main transcript	c.886-122T>C		intron_variant		ENST00000582621.6	NP_001290547.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD226	ENST00000582621.6 linkuse as main transcript	c.886-122T>C		intron_variant		1	NM_001303618.2	ENSP00000461947	P1

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56255

AN:

151982

Hom.:

10610

Cov.:

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.348

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.402

GnomAD4 exome

AF:

0.400

AC:

307951

AN:

770108

Hom.:

62461

AF XY:

0.402

AC XY:

159372

AN XY:

396058

show subpopulations

Gnomad4 AFR exome

AF:

0.368

Gnomad4 AMR exome

AF:

0.350

Gnomad4 ASJ exome

AF:

0.406

Gnomad4 EAS exome

AF:

0.258

Gnomad4 SAS exome

AF:

0.426

Gnomad4 FIN exome

AF:

0.320

Gnomad4 NFE exome

AF:

0.414

Gnomad4 OTH exome

AF:

0.397

GnomAD4 genome

AF:

0.370

AC:

56310

AN:

152100

Hom.:

10624

Cov.:

AF XY:

0.364

AC XY:

27090

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.355

Gnomad4 AMR

AF:

0.349

Gnomad4 ASJ

AF:

0.373

Gnomad4 EAS

AF:

0.242

Gnomad4 SAS

AF:

0.409

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.400

Gnomad4 OTH

AF:

0.403

Alfa

AF:

0.366

Hom.:

1250

Bravo

AF:

0.377

Asia WGS

AF:

0.320

AC:

1119

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.79

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over