rs62090790

Variant names:

• chr18-69867472-G-A
• rs62090790
• NM_001303618.2:c.831-61C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-69867472-G-A
• chr18-69867472-G-C
• chr18-69867472-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001303618.2(CD226):​c.831-61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0275 in 1,088,650 control chromosomes in the GnomAD database, including 511 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 0.027 (68 hom., cov: 32)
  • Exomes 𝑓: 0.028 (443 hom.)
• Consequence: CD226 NM_001303618.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0267 (4053/152056) while in subpopulation NFE AF = 0.0307 (2086/67996). AF 95% confidence interval is 0.0296. There are 68 homozygotes in GnomAd4. There are 1938 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 68 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303618.2. 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
	CD226	NM_001303618.2	MANE Select	c.831-61C>T		intron	N/A	NP_001290547.1	Q15762
	CD226	NM_006566.4		c.831-61C>T		intron	N/A	NP_006557.2	Q15762
	CD226	NM_001303619.2		c.366-61C>T		intron	N/A	NP_001290548.1	J3QR77

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD226	ENST00000582621.6	TSL:1 MANE Select	c.831-61C>T		intron	N/A	ENSP00000461947.1	Q15762
	CD226	ENST00000280200.8	TSL:1	c.831-61C>T		intron	N/A	ENSP00000280200.4	Q15762
	CD226	ENST00000581982.5	TSL:1	c.366-61C>T		intron	N/A	ENSP00000464084.1	J3QR77

Frequencies

GnomAD3 genomes AF: 0.0266 AC: 4043 AN: 151938 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0258

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0226

GnomAD4 exome AF: 0.0276 AC: 25858 AN: 936594 Hom.: 443 AF XY: 0.0276 AC XY: 13490 AN XY: 489294

African (AFR) AF: 0.0318 AC: 750 AN: 23550

American (AMR) AF: 0.0121 AC: 530 AN: 43834

Ashkenazi Jewish (ASJ) AF: 0.00939 AC: 214 AN: 22796

East Asian (EAS) AF: 0.00401 AC: 150 AN: 37440

South Asian (SAS) AF: 0.0238 AC: 1795 AN: 75504

European-Finnish (FIN) AF: 0.0285 AC: 1360 AN: 47740

Middle Eastern (MID) AF: 0.0189 AC: 90 AN: 4768

European-Non Finnish (NFE) AF: 0.0311 AC: 19805 AN: 637674

Other (OTH) AF: 0.0269 AC: 1164 AN: 43288

GnomAD4 genome AF: 0.0267 AC: 4053 AN: 152056 Hom.: 68 Cov.: 32 AF XY: 0.0261 AC XY: 1938 AN XY: 74336

African (AFR) AF: 0.0291 AC: 1208 AN: 41474

American (AMR) AF: 0.0103 AC: 157 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5180

South Asian (SAS) AF: 0.0260 AC: 125 AN: 4804

European-Finnish (FIN) AF: 0.0282 AC: 297 AN: 10550

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2086 AN: 67996

Other (OTH) AF: 0.0223 AC: 47 AN: 2106

Alfa AF: 0.0257 Hom.: 9

Bravo AF: 0.0255

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.39
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs62090790; hg19: chr18-67534708; COSMIC: COSV54615440;