chr17-47304457-G-T

Variant names:

• chr17-47304457-G-T
• rs11869835
• NM_000212.3:c.2134+1617G>T

Variant summary

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

The NM_000212.3(ITGB3):​c.2134+1617G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,308 control chromosomes in the GnomAD database, including 605 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 0.086 (605 hom., cov: 32)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 9 publications found

Genes affected

ITGB3 (HGNC:6156): (integrin subunit beta 3) The ITGB3 protein product is the integrin beta chain beta 3. Integrins are integral cell-surface proteins composed of an alpha chain and a beta chain. A given chain may combine with multiple partners resulting in different integrins. Integrin beta 3 is found along with the alpha IIb chain in platelets. Integrins are known to participate in cell adhesion as well as cell-surface mediated signalling. [provided by RefSeq, Jul 2008]

ENSG00000259753 (HGNC:):

EFCAB13-DT (HGNC:55338): (EFCAB13 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB3	NM_000212.3	c.2134+1617G>T		intron_variant	Intron 13 of 14	ENST00000559488.7	NP_000203.2
EFCAB13-DT	NR_110880.1	n.363-675C>A		intron_variant	Intron 2 of 2
EFCAB13-DT	NR_110881.1	n.227-675C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7	c.2134+1617G>T		intron_variant	Intron 13 of 14	1	NM_000212.3	ENSP00000452786.2
ENSG00000259753	ENST00000560629.1	n.2098+1617G>T		intron_variant	Intron 13 of 17	2		ENSP00000456711.2

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13047 AN: 152190 Hom.: 604 Cov.: 32

Gnomad AFR AF: 0.0963

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0857 AC: 13058 AN: 152308 Hom.: 605 Cov.: 32 AF XY: 0.0852 AC XY: 6349 AN XY: 74488

African (AFR) AF: 0.0961 AC: 3995 AN: 41562

American (AMR) AF: 0.0836 AC: 1279 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3472

East Asian (EAS) AF: 0.192 AC: 995 AN: 5182

South Asian (SAS) AF: 0.119 AC: 574 AN: 4832

European-Finnish (FIN) AF: 0.0352 AC: 374 AN: 10620

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0726 AC: 4935 AN: 68020

Other (OTH) AF: 0.0971 AC: 205 AN: 2112

Alfa AF: 0.0777 Hom.: 271

Bravo AF: 0.0908

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		0.050
Mutation Taster		=100/0	polymorphism (auto)

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: rs11869835; hg19: chr17-45381823;