rs13306487

Variant names:

• chr17-47292422-G-A
• rs13306487
• NM_000212.3:c.1544G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-47292422-G-A
• chr17-47292422-G-C
• chr17-47292422-G-T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BA1 BP4

This summary comes from the ClinGen Evidence Repository: The NM_000212.3(ITGB3):c.1544G>A (p.Arg515Gln) missense variant occurs at an allele frequency of 0.02211 in the gnomAD East Asian population and is predicted, by REVEL score of 0.183, to have no impact on the gene or gene product. This variant has been reported in the literature multiple times (including PMIDs: 7694683 and 8457479) as the alloantigenic site HPA-6 (formerly known as Ca/Tu). In summary, the variant is classified as benign for GT. GT-specific criteria applied: BA1 and BP4. LINK:https://erepo.genome.network/evrepo/ui/classification/CA123241/MONDO:0010119/011

• Frequency:
  • Genomes: 𝑓 0.0016 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0011 (8 hom.)
• Consequence: ITGB3 NM_000212.3 missense
• Clinical Significance: Benign reviewed by expert panel U:1 B:4
• Conservation: PhyloP100: -0.931
• Publications: 12 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 -9 ACMG points.

• BP4: 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.1544G>A	p.Arg515Gln	missense	Exon 10 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.1544G>A	p.Arg515Gln	missense	Exon 10 of 15	ENSP00000452786.2	P05106-1
	ENSG00000259753	ENST00000560629.1	TSL:2	n.1508G>A		non_coding_transcript_exon	Exon 10 of 18	ENSP00000456711.2	H3BM21
	ITGB3	ENST00000696963.1		c.1544G>A	p.Arg515Gln	missense	Exon 10 of 14	ENSP00000513002.1	P05106-2

Frequencies

GnomAD3 genomes AF: 0.00159 AC: 242 AN: 152234 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00894

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000426

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00270 AC: 675 AN: 250376 AF XY: 0.00254

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.0000579

Gnomad ASJ exome AF: 0.000301

Gnomad EAS exome AF: 0.0219

Gnomad FIN exome AF: 0.00981

Gnomad NFE exome AF: 0.000389

Gnomad OTH exome AF: 0.00115

GnomAD4 exome AF: 0.00109 AC: 1597 AN: 1459212 Hom.: 8 Cov.: 37 AF XY: 0.00105 AC XY: 760 AN XY: 725372

African (AFR) AF: 0.0000299 AC: 1 AN: 33444

American (AMR) AF: 0.0000448 AC: 2 AN: 44690

Ashkenazi Jewish (ASJ) AF: 0.000307 AC: 8 AN: 26056

East Asian (EAS) AF: 0.0194 AC: 770 AN: 39630

South Asian (SAS) AF: 0.000313 AC: 27 AN: 86194

European-Finnish (FIN) AF: 0.00938 AC: 500 AN: 53328

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5756

European-Non Finnish (NFE) AF: 0.000130 AC: 144 AN: 1109832

Other (OTH) AF: 0.00241 AC: 145 AN: 60282

GnomAD4 genome AF: 0.00158 AC: 241 AN: 152352 Hom.: 1 Cov.: 33 AF XY: 0.00201 AC XY: 150 AN XY: 74506

African (AFR) AF: 0.0000240 AC: 1 AN: 41582

American (AMR) AF: 0.000392 AC: 6 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5180

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.00894 AC: 95 AN: 10626

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

European-Non Finnish (NFE) AF: 0.000426 AC: 29 AN: 68042

Other (OTH) AF: 0.00236 AC: 5 AN: 2116

Alfa AF: 0.000381 Hom.: 0

Bravo AF: 0.00125

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.00232 AC: 282

Asia WGS AF: 0.0120 AC: 42 AN: 3478

EpiCase AF: 0.000109

EpiControl AF: 0.000237

ClinVar

ClinVar submissions

Significance: Benign

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
-	1	1	Glanzmann thrombasthenia (2)
-	-	2	not provided (2)
-	-	1	Ca/Tu ALLOANTIGEN POLYMORPHISM (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.065
BayesDel_addAF	Benign	-0.49	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	10
DANN	Benign	0.97
DEOGEN2	Benign	0.28	T
Eigen	Benign	-0.88
Eigen_PC	Benign	-0.77
FATHMM_MKL	Benign	0.10	N
LIST_S2	Benign	0.74	T
MetaRNN	Benign	0.0033	T
MetaSVM	Benign	-0.84	T
MutationAssessor	Benign	0.10	N
PhyloP100		-0.93
PrimateAI	Benign	0.19	T
PROVEAN	Benign	0.45	N
Sift	Benign	0.47	T
Sift4G	Benign	0.59	T
Polyphen		0.0	B
Vest4		0.086
MVP		0.81
MPC		0.47
ClinPred		0.016	T
GERP RS		-0.14
Varity_R		0.057
gMVP		0.39
Mutation Taster		=93/7	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: rs13306487; hg19: chr17-45369788; COSMIC: COSV71384128; COSMIC: COSV71384128;