Variant 10-32920338-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_002211.4(ITGB1):c.1176C>A(p.Gly392=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 1,611,972 control chromosomes in the GnomAD database, including 620,981 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.82 ( 52461 hom., cov: 32)

Exomes 𝑓: 0.88 ( 568520 hom. )

Consequence

ITGB1
NM_002211.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.562

Variant links:

Genes affected

ITGB1 (HGNC:6153): (integrin subunit beta 1) Integrins are heterodimeric proteins made up of alpha and beta subunits. At least 18 alpha and 8 beta subunits have been described in mammals. Integrin family members are membrane receptors involved in cell adhesion and recognition in a variety of processes including embryogenesis, hemostasis, tissue repair, immune response and metastatic diffusion of tumor cells. This gene encodes a beta subunit. Multiple alternatively spliced transcript variants which encode different protein isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ITGB1 links:

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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=-0.45).

BP6

Variant 10-32920338-G-T is Benign according to our data. Variant chr10-32920338-G-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.562 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ITGB1	NM_002211.4 linkuse as main transcript	c.1176C>A	p.Gly392=	synonymous_variant	10/16	ENST00000302278.8
ITGB1	NM_033668.2 linkuse as main transcript	c.1176C>A	p.Gly392=	synonymous_variant	9/16
ITGB1	NM_133376.3 linkuse as main transcript	c.1176C>A	p.Gly392=	synonymous_variant	10/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB1	ENST00000302278.8 linkuse as main transcript	c.1176C>A	p.Gly392=	synonymous_variant	10/16	1	NM_002211.4	P4	P05556-1

Frequencies

GnomAD3 genomes

AF:

0.825

AC:

125357

AN:

151984

Hom.:

52424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.678

Gnomad AMI

AF:

0.958

Gnomad AMR

AF:

0.873

Gnomad ASJ

AF:

0.909

Gnomad EAS

AF:

0.675

Gnomad SAS

AF:

0.864

Gnomad FIN

AF:

0.879

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.897

Gnomad OTH

AF:

0.836

GnomAD3 exomes

AF:

0.861

AC:

216033

AN:

251006

Hom.:

93726

AF XY:

0.863

AC XY:

117107

AN XY:

135650

show subpopulations

Gnomad AFR exome

AF:

0.676

Gnomad AMR exome

AF:

0.907

Gnomad ASJ exome

AF:

0.905

Gnomad EAS exome

AF:

0.679

Gnomad SAS exome

AF:

0.871

Gnomad FIN exome

AF:

0.875

Gnomad NFE exome

AF:

0.892

Gnomad OTH exome

AF:

0.872

GnomAD4 exome

AF:

0.881

AC:

1286242

AN:

1459868

Hom.:

568520

Cov.:

AF XY:

0.881

AC XY:

639955

AN XY:

726420

show subpopulations

Gnomad4 AFR exome

AF:

0.665

Gnomad4 AMR exome

AF:

0.903

Gnomad4 ASJ exome

AF:

0.906

Gnomad4 EAS exome

AF:

0.689

Gnomad4 SAS exome

AF:

0.871

Gnomad4 FIN exome

AF:

0.875

Gnomad4 NFE exome

AF:

0.895

Gnomad4 OTH exome

AF:

0.870

GnomAD4 genome

AF:

0.825

AC:

125446

AN:

152104

Hom.:

52461

Cov.:

AF XY:

0.824

AC XY:

61236

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.678

Gnomad4 AMR

AF:

0.873

Gnomad4 ASJ

AF:

0.909

Gnomad4 EAS

AF:

0.675

Gnomad4 SAS

AF:

0.865

Gnomad4 FIN

AF:

0.879

Gnomad4 NFE

AF:

0.897

Gnomad4 OTH

AF:

0.838

Alfa

AF:

0.877

Hom.:

72805

Bravo

AF:

0.818

Asia WGS

AF:

0.819

AC:

2849

AN:

3478

EpiCase

AF:

0.894

EpiControl

AF:

0.893

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

5.7

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over