rs3760372

Variant names:

• chr17-47302636-T-C
• rs3760372
• NM_000212.3:c.2015-85T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-47302636-T-C
• chr17-47302636-T-A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000212.3(ITGB3):​c.2015-85T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 1,529,136 control chromosomes in the GnomAD database, including 369,405 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.71 (38726 hom., cov: 32)
  • Exomes 𝑓: 0.69 (330679 hom.)
• Consequence: ITGB3 NM_000212.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.00500
• Publications: 21 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 17-47302636-T-C is Benign according to our data. Variant chr17-47302636-T-C is described in ClinVar as Benign. ClinVar VariationId is 1271035.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000212.3. 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
	ITGB3	NM_000212.3	MANE Select	c.2015-85T>C		intron	N/A	NP_000203.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB3	ENST00000559488.7	TSL:1 MANE Select	c.2015-85T>C		intron	N/A	ENSP00000452786.2	P05106-1
	ENSG00000259753	ENST00000560629.1	TSL:2	n.1979-85T>C		intron	N/A	ENSP00000456711.2	H3BM21
	ITGB3	ENST00000696963.1		c.2015-85T>C		intron	N/A	ENSP00000513002.1	P05106-2

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108015 AN: 151980 Hom.: 38701 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.710

GnomAD4 exome AF: 0.692 AC: 952798 AN: 1377038 Hom.: 330679 AF XY: 0.694 AC XY: 478453 AN XY: 689414

African (AFR) AF: 0.769 AC: 24453 AN: 31812

American (AMR) AF: 0.559 AC: 24593 AN: 43986

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 17829 AN: 25560

East Asian (EAS) AF: 0.831 AC: 32571 AN: 39194

South Asian (SAS) AF: 0.742 AC: 61989 AN: 83586

European-Finnish (FIN) AF: 0.668 AC: 35184 AN: 52682

Middle Eastern (MID) AF: 0.725 AC: 4010 AN: 5532

European-Non Finnish (NFE) AF: 0.686 AC: 711290 AN: 1037122

Other (OTH) AF: 0.710 AC: 40879 AN: 57564

GnomAD4 genome AF: 0.711 AC: 108091 AN: 152098 Hom.: 38726 Cov.: 32 AF XY: 0.708 AC XY: 52630 AN XY: 74356

African (AFR) AF: 0.770 AC: 31930 AN: 41484

American (AMR) AF: 0.634 AC: 9697 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2509 AN: 3470

East Asian (EAS) AF: 0.815 AC: 4217 AN: 5172

South Asian (SAS) AF: 0.733 AC: 3531 AN: 4816

European-Finnish (FIN) AF: 0.667 AC: 7044 AN: 10568

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46783 AN: 67988

Other (OTH) AF: 0.707 AC: 1491 AN: 2110

Alfa AF: 0.682 Hom.: 15691

Bravo AF: 0.711

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.45
PhyloP100		0.0050
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: rs3760372; hg19: chr17-45380002; COSMIC: COSV71385006; COSMIC: COSV71385006;