ENST00000414157.3:n.279+20085G>A

Variant names:

• chr10-33005847-G-A
• rs11009175
• ENST00000414157.3:n.279+20085G>A

Variant summary

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

The ENST00000414157.3(ITGB1-DT):​n.279+20085G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,158 control chromosomes in the GnomAD database, including 1,077 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 0.11 (1077 hom., cov: 32)
  • Exomes 𝑓: 0.048 (0 hom.)
• Consequence: ITGB1-DT ENST00000414157.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 16 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1-DT	NR_184020.1	n.270+20090G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000414157.3	n.279+20085G>A		intron_variant	Intron 2 of 2	1
ITGB1-DT	ENST00000450890.6	n.620+20090G>A		intron_variant	Intron 3 of 3	3
ITGB1-DT	ENST00000666298.2	n.783+20090G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16048 AN: 151998 Hom.: 1078 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.0476 AC: 2 AN: 42 Hom.: 0 AF XY: 0.0294 AC XY: 1 AN XY: 34

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0556 AC: 2 AN: 36

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.106 AC: 16053 AN: 152116 Hom.: 1077 Cov.: 32 AF XY: 0.106 AC XY: 7886 AN XY: 74364

African (AFR) AF: 0.0340 AC: 1411 AN: 41528

American (AMR) AF: 0.112 AC: 1716 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 473 AN: 3462

East Asian (EAS) AF: 0.197 AC: 1008 AN: 5124

South Asian (SAS) AF: 0.148 AC: 713 AN: 4822

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10618

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8986 AN: 67970

Other (OTH) AF: 0.126 AC: 266 AN: 2104

Alfa AF: 0.127 Hom.: 1155

Bravo AF: 0.101

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.6
DANN	Benign	0.88
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs11009175; hg19: chr10-33294775;