rs941831

Variant names:

• chr10-33035588-A-G
• rs941831
• ENST00000414157.2:n.276-45754A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000423444.1(ENSG00000229878):​n.77T>C variant causes a non coding transcript exon 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: ENSG00000229878 ENST00000423444.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.69

Genes affected

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

ENSG00000229878 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000414157.2	n.276-45754A>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	ENST00000450890.5	n.288-45754A>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

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

Gnomad4 AFR AF: 0.0329

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.0425

Gnomad4 FIN AF: 0.00858

Gnomad4 NFE AF: 0.0287

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0410 Hom.: 313

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941831; hg19: chr10-33324516;