rs2292863

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000212.3(ITGB3):​c.1261-375C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,046 control chromosomes in the GnomAD database, including 6,391 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 0.29 ( 6391 hom., cov: 32)

Consequence

ITGB3
NM_000212.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.359
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ITGB3NM_000212.3 linkuse as main transcriptc.1261-375C>G intron_variant ENST00000559488.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ITGB3ENST00000559488.7 linkuse as main transcriptc.1261-375C>G intron_variant 1 NM_000212.3 P1P05106-1
ITGB3ENST00000573377.1 linkuse as main transcriptc.*267+337C>G intron_variant, NMD_transcript_variant 1
ITGB3ENST00000696963.1 linkuse as main transcriptc.1261-375C>G intron_variant P05106-2

Frequencies

GnomAD3 genomes
AF:
0.286
AC:
43509
AN:
151928
Hom.:
6382
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.265
Gnomad AMI
AF:
0.265
Gnomad AMR
AF:
0.280
Gnomad ASJ
AF:
0.282
Gnomad EAS
AF:
0.332
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.283
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.297
Gnomad OTH
AF:
0.307
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.286
AC:
43541
AN:
152046
Hom.:
6391
Cov.:
32
AF XY:
0.286
AC XY:
21245
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.265
Gnomad4 AMR
AF:
0.280
Gnomad4 ASJ
AF:
0.282
Gnomad4 EAS
AF:
0.332
Gnomad4 SAS
AF:
0.294
Gnomad4 FIN
AF:
0.283
Gnomad4 NFE
AF:
0.297
Gnomad4 OTH
AF:
0.304
Alfa
AF:
0.288
Hom.:
818
Bravo
AF:
0.282
Asia WGS
AF:
0.337
AC:
1173
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
4.3
DANN
Benign
0.78

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2292863; hg19: chr17-45369130; API