rs941831

Variant names:

• chr10-33035588-A-G
• rs941831
• ENST00000414157.3:n.280-45754A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000414157.3(ITGB1-DT):​n.280-45754A>G variant causes a intron change. The variant allele was found at a frequency of 0.0508 in 152,216 control chromosomes in the GnomAD database, including 483 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 0.051 (483 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ITGB1-DT ENST00000414157.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.69
• Publications: 2 publications found

Genes affected

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

ENSG00000229878 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGB1-DT	NR_184020.1	n.271-45754A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000414157.3	n.280-45754A>G		intron_variant	Intron 2 of 2	1
ENSG00000229878	ENST00000423444.1	n.77T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ITGB1-DT	ENST00000450890.6	n.621-45754A>G		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7719 AN: 152098 Hom.: 479 Cov.: 31

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.00858

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0607

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0508 AC: 7738 AN: 152216 Hom.: 483 Cov.: 31 AF XY: 0.0542 AC XY: 4030 AN XY: 74422

African (AFR) AF: 0.0329 AC: 1365 AN: 41524

American (AMR) AF: 0.166 AC: 2542 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5164

South Asian (SAS) AF: 0.0425 AC: 205 AN: 4822

European-Finnish (FIN) AF: 0.00858 AC: 91 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0287 AC: 1950 AN: 68018

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0431 Hom.: 429

Bravo AF: 0.0635

Asia WGS AF: 0.156 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.88
PhyloP100		6.7

Splicing

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

Other links and lift over

dbSNP: rs941831; hg19: chr10-33324516;