rs5920

Variant names:

• chr17-47283530-T-C
• rs5920
• NM_000212.3:c.342T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-47283530-T-C
• chr17-47283530-T-A
• chr17-47283530-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP7 BA1 BP4

This summary comes from the ClinGen Evidence Repository: The NM_000212.2:c.342T>C variant, which leads to a synonymous change, Ile114Ile, is reported at a high frequency in the African population in gnomAD and ExAC (0.05). In-silico splicing predictors do not predict splicing impact. PMID:27469266 reports on this and other polymorphic, non-causal variants found in linkage disequilibrium with deleterious mutations in GT patients. Ile114Ile is classified as a benign variant. GT-specific criteria applied: BA1, BP4, and BP7. LINK:https://erepo.genome.network/evrepo/ui/classification/CA8622916/MONDO:0010119/011

• Frequency:
  • Genomes: 𝑓 0.016 (90 hom., cov: 32)
  • Exomes 𝑓: 0.0017 (52 hom.)
• Consequence: ITGB3 NM_000212.3 synonymous
• Clinical Significance: Benign reviewed by expert panel B:5
• Conservation: PhyloP100: -0.560
• Publications: 7 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 -10 ACMG points.

• BP4: For more information check the summary or visit ClinGen Evidence Repository.
• BP7: For more information check the summary or visit ClinGen Evidence Repository.
• BA1: For more information check the summary or visit ClinGen Evidence Repository.

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.342T>C	p.Ile114Ile	synonymous	Exon 3 of 15	NP_000203.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB3	ENST00000559488.7	TSL:1 MANE Select	c.342T>C	p.Ile114Ile	synonymous	Exon 3 of 15	ENSP00000452786.2	P05106-1
	ITGB3	ENST00000571680.1	TSL:1	c.342T>C	p.Ile114Ile	synonymous	Exon 3 of 9	ENSP00000461626.1	I3L4X8
	ENSG00000259753	ENST00000560629.1	TSL:2	n.306T>C		non_coding_transcript_exon	Exon 3 of 18	ENSP00000456711.2	H3BM21

Frequencies

GnomAD3 genomes AF: 0.0161 AC: 2446 AN: 152184 Hom.: 84 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00995

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.0134

GnomAD2 exomes AF: 0.00441 AC: 1105 AN: 250394 AF XY: 0.00336

Gnomad AFR exome AF: 0.0545

Gnomad AMR exome AF: 0.00465

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000311

Gnomad OTH exome AF: 0.00359

GnomAD4 exome AF: 0.00173 AC: 2524 AN: 1461892 Hom.: 52 Cov.: 33 AF XY: 0.00149 AC XY: 1082 AN XY: 727248

African (AFR) AF: 0.0538 AC: 1802 AN: 33480

American (AMR) AF: 0.00503 AC: 225 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0000383 AC: 1 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000104 AC: 9 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00919 AC: 53 AN: 5768

European-Non Finnish (NFE) AF: 0.000158 AC: 176 AN: 1112010

Other (OTH) AF: 0.00427 AC: 258 AN: 60396

GnomAD4 genome AF: 0.0163 AC: 2475 AN: 152302 Hom.: 90 Cov.: 32 AF XY: 0.0154 AC XY: 1145 AN XY: 74466

African (AFR) AF: 0.0547 AC: 2272 AN: 41550

American (AMR) AF: 0.00993 AC: 152 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000294 AC: 20 AN: 68036

Other (OTH) AF: 0.0132 AC: 28 AN: 2114

Alfa AF: 0.0126 Hom.: 64

Bravo AF: 0.0185

Asia WGS AF: 0.00433 AC: 15 AN: 3478

EpiCase AF: 0.000327

EpiControl AF: 0.000652

ClinVar

ClinVar submissions

Significance: Benign

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
-	-	2	Glanzmann thrombasthenia (2)
-	-	2	not provided (2)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	9.0
DANN	Benign	0.76
PhyloP100		-0.56
Mutation Taster		=98/2	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: rs5920; hg19: chr17-45360896; COSMIC: COSV99068316; COSMIC: COSV99068316;