rs11869835

chr17-47304457-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ITGB3	NM_000212.3	c.2134+1617G>T		intron_variant		ENST00000559488.7
EFCAB13-DT	NR_110880.1	n.363-675C>A		intron_variant, non_coding_transcript_variant
EFCAB13-DT	NR_110881.1	n.227-675C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB3	ENST00000559488.7	c.2134+1617G>T		intron_variant		1	NM_000212.3	P1
EFCAB13-DT	ENST00000575039.1	n.227-675C>A		intron_variant, non_coding_transcript_variant		5
ITGB3	ENST00000696963.1	c.2134+1617G>T		intron_variant
EFCAB13-DT	ENST00000576345.2	n.165-675C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.0971

Alfa AF: 0.0774 Hom.: 242

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

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

Other links and lift over

dbSNP: rs11869835; hg19: chr17-45381823;