rs2230394

Variant names:

• chr10-32928182-G-A
• rs2230394
• NM_002211.4:c.459C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-32928182-G-A
• chr10-32928182-G-C
• chr10-32928182-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_002211.4(ITGB1):​c.459C>T​(p.Tyr153Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,336,250 control chromosomes in the GnomAD database, including 12,308 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 0.16 (2398 hom., cov: 33)
  • Exomes 𝑓: 0.12 (9910 hom.)
• Consequence: ITGB1 NM_002211.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.32

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP7: Synonymous conserved (PhyloP=2.32 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1	NM_002211.4	c.459C>T	p.Tyr153Tyr	synonymous_variant	Exon 5 of 16	ENST00000302278.8	NP_002202.2
ITGB1	NM_033668.2	c.459C>T	p.Tyr153Tyr	synonymous_variant	Exon 4 of 16		NP_391988.1
ITGB1	NM_133376.3	c.459C>T	p.Tyr153Tyr	synonymous_variant	Exon 5 of 16		NP_596867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1	ENST00000302278.8	c.459C>T	p.Tyr153Tyr	synonymous_variant	Exon 5 of 16	1	NM_002211.4	ENSP00000303351.3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24216 AN: 152002 Hom.: 2396 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.152

GnomAD3 exomes AF: 0.134 AC: 33512 AN: 250538 Hom.: 2872 AF XY: 0.132 AC XY: 17888 AN XY: 135392

Gnomad AFR exome AF: 0.265

Gnomad AMR exome AF: 0.0876

Gnomad ASJ exome AF: 0.0947

Gnomad EAS exome AF: 0.321

Gnomad SAS exome AF: 0.126

Gnomad FIN exome AF: 0.125

Gnomad NFE exome AF: 0.107

Gnomad OTH exome AF: 0.125

GnomAD4 exome AF: 0.121 AC: 143738 AN: 1184130 Hom.: 9910 Cov.: 20 AF XY: 0.121 AC XY: 72929 AN XY: 602492

Gnomad4 AFR exome AF: 0.275

Gnomad4 AMR exome AF: 0.0916

Gnomad4 ASJ exome AF: 0.0955

Gnomad4 EAS exome AF: 0.311

Gnomad4 SAS exome AF: 0.127

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.129

GnomAD4 genome AF: 0.159 AC: 24229 AN: 152120 Hom.: 2398 Cov.: 33 AF XY: 0.161 AC XY: 11942 AN XY: 74360

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0917

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.150

Alfa AF: 0.116 Hom.: 1014

Bravo AF: 0.163

Asia WGS AF: 0.177 AC: 614 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.6
DANN	Benign	0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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

Other links and lift over

dbSNP: rs2230394; hg19: chr10-33217110; COSMIC: COSV56479684; COSMIC: COSV56479684;