17-47311220-T-A

Variant names:

• chr17-47311220-T-A
• rs3809865
• NM_000212.3:c.*1016T>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.*1016T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 154,644 control chromosomes in the GnomAD database, including 38,174 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.70 (37521 hom., cov: 31)
  • Exomes 𝑓: 0.70 (653 hom.)
• Consequence: ITGB3 NM_000212.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.361
• Publications: 35 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=-0.8).
• BP6: Variant 17-47311220-T-A is Benign according to our data. Variant chr17-47311220-T-A is described in ClinVar as Benign. ClinVar VariationId is 323891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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.*1016T>A		3_prime_UTR	Exon 15 of 15	NP_000203.2
	EFCAB13-DT	NR_110880.1		n.362+7252A>T		intron	N/A
	EFCAB13-DT	NR_110881.1		n.226+7252A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB3	ENST00000559488.7	TSL:1 MANE Select	c.*1016T>A		3_prime_UTR	Exon 15 of 15	ENSP00000452786.2	P05106-1
	ENSG00000259753	ENST00000560629.1	TSL:2	n.2265+3583T>A		intron	N/A	ENSP00000456711.2	H3BM21
	EFCAB13-DT	ENST00000575039.1	TSL:5	n.226+7252A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106432 AN: 151930 Hom.: 37502 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.707

GnomAD4 exome AF: 0.701 AC: 1820 AN: 2596 Hom.: 653 Cov.: 0 AF XY: 0.705 AC XY: 1024 AN XY: 1452

African (AFR) AF: 0.660 AC: 33 AN: 50

American (AMR) AF: 0.519 AC: 27 AN: 52

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 45 AN: 64

East Asian (EAS) AF: 0.768 AC: 232 AN: 302

South Asian (SAS) AF: 0.500 AC: 3 AN: 6

European-Finnish (FIN) AF: 0.694 AC: 500 AN: 720

Middle Eastern (MID) AF: 0.500 AC: 4 AN: 8

European-Non Finnish (NFE) AF: 0.696 AC: 891 AN: 1280

Other (OTH) AF: 0.746 AC: 85 AN: 114

GnomAD4 genome AF: 0.700 AC: 106501 AN: 152048 Hom.: 37521 Cov.: 31 AF XY: 0.699 AC XY: 51950 AN XY: 74318

African (AFR) AF: 0.717 AC: 29716 AN: 41462

American (AMR) AF: 0.632 AC: 9668 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4158 AN: 5150

South Asian (SAS) AF: 0.736 AC: 3543 AN: 4812

European-Finnish (FIN) AF: 0.691 AC: 7305 AN: 10578

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47242 AN: 67978

Other (OTH) AF: 0.704 AC: 1486 AN: 2110

Alfa AF: 0.593 Hom.: 1688

Bravo AF: 0.696

Asia WGS AF: 0.725 AC: 2518 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		0.36
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: rs3809865; hg19: chr17-45388586;