chr10-32920338-G-T

Position:

• chr10-32920338-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6 BP7 BA1

The NM_002211.4(ITGB1):​c.1176C>A​(p.Gly392Gly) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562

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 (HGNC:):

ACMG classification

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	Protein	UniProt
ITGB1	NM_002211.4	c.1176C>A	p.Gly392Gly	synonymous_variant	10/16	ENST00000302278.8	NP_002202.2
ITGB1	NM_033668.2	c.1176C>A	p.Gly392Gly	synonymous_variant	9/16		NP_391988.1
ITGB1	NM_133376.3	c.1176C>A	p.Gly392Gly	synonymous_variant	10/16		NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.1176C>A	p.Gly392Gly	synonymous_variant	10/16	1	NM_002211.4	ENSP00000303351.3

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125357 AN: 151984 Hom.: 52424 Cov.: 32

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

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.: 37 AF XY: 0.881 AC XY: 639955 AN XY: 726420

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.: 32 AF XY: 0.824 AC XY: 61236 AN XY: 74358

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

Other links and lift over

dbSNP: rs2230396; hg19: chr10-33209266; COSMIC: COSV56480050;