10-32988854-C-T

Variant names:

• chr10-32988854-C-T
• rs10827167
• ENST00000414157.3:n.279+3092C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000534049.5(ITGB1):​c.-1+3477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 149,330 control chromosomes in the GnomAD database, including 8,423 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 0.33 (8423 hom., cov: 28)
• Consequence: ITGB1 ENST00000534049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 6 publications found

Genes affected

ITGB1-DT (HGNC:53718): (ITGB1 divergent transcript)

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534049.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1-DT	NR_184020.1		n.270+3097C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1-DT	ENST00000414157.3	TSL:1	n.279+3092C>T		intron	N/A
	ITGB1	ENST00000534049.5	TSL:4	c.-1+3477G>A		intron	N/A	ENSP00000431326.1
	ITGB1-DT	ENST00000450890.6	TSL:3	n.620+3097C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 49706 AN: 149242 Hom.: 8411 Cov.: 28

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.333 AC: 49736 AN: 149330 Hom.: 8423 Cov.: 28 AF XY: 0.336 AC XY: 24381 AN XY: 72612

African (AFR) AF: 0.385 AC: 15586 AN: 40494

American (AMR) AF: 0.276 AC: 4082 AN: 14816

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1024 AN: 3458

East Asian (EAS) AF: 0.429 AC: 2171 AN: 5064

South Asian (SAS) AF: 0.432 AC: 2034 AN: 4712

European-Finnish (FIN) AF: 0.326 AC: 3190 AN: 9792

Middle Eastern (MID) AF: 0.344 AC: 99 AN: 288

European-Non Finnish (NFE) AF: 0.303 AC: 20521 AN: 67720

Other (OTH) AF: 0.334 AC: 695 AN: 2078

Alfa AF: 0.312 Hom.: 11840

Bravo AF: 0.332

Asia WGS AF: 0.435 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.36
PhyloP100		-0.10

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10827167; hg19: chr10-33277782;