10-33129944-G-A

Variant names:

• chr10-33129944-G-A
• rs2666236
• ENST00000821378.1:n.574-4624G>A

Variant summary

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

The ENST00000821378.1(ITGB1-DT):​n.574-4624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,922 control chromosomes in the GnomAD database, including 19,842 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 0.50 (19842 hom., cov: 32)
• Consequence: ITGB1-DT ENST00000821378.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 12 publications found

Genes affected

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

ENSG00000306881 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821378.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGB1-DT	ENST00000821378.1		n.574-4624G>A		intron	N/A
	ITGB1-DT	ENST00000821379.1		n.405-4624G>A		intron	N/A
	ITGB1-DT	ENST00000821403.1		n.97-4624G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76023 AN: 151804 Hom.: 19818 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.501 AC: 76086 AN: 151922 Hom.: 19842 Cov.: 32 AF XY: 0.500 AC XY: 37165 AN XY: 74258

African (AFR) AF: 0.613 AC: 25375 AN: 41426

American (AMR) AF: 0.507 AC: 7743 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3464

East Asian (EAS) AF: 0.751 AC: 3863 AN: 5142

South Asian (SAS) AF: 0.558 AC: 2679 AN: 4804

European-Finnish (FIN) AF: 0.369 AC: 3891 AN: 10534

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29139 AN: 67960

Other (OTH) AF: 0.514 AC: 1084 AN: 2110

Alfa AF: 0.475 Hom.: 6519

Bravo AF: 0.516

Asia WGS AF: 0.642 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.65
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2666236; hg19: chr10-33418872;