6-132625583-T-C

Variant names:

• chr6-132625583-T-C
• rs4380767
• ENST00000466706.2:n.170+8045A>G

Variant summary

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

The ENST00000466706.2(ENSG00000290584):​n.170+8045A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,948 control chromosomes in the GnomAD database, including 43,390 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 0.74 (43390 hom., cov: 31)
• Consequence: ENSG00000290584 ENST00000466706.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 1 publications found

Genes affected

ENSG00000290584 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290584	ENST00000466706.2	n.170+8045A>G		intron_variant	Intron 1 of 2	6

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112937 AN: 151828 Hom.: 43326 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.744 AC: 113062 AN: 151948 Hom.: 43390 Cov.: 31 AF XY: 0.745 AC XY: 55349 AN XY: 74260

African (AFR) AF: 0.933 AC: 38686 AN: 41482

American (AMR) AF: 0.633 AC: 9652 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2311 AN: 3470

East Asian (EAS) AF: 0.916 AC: 4730 AN: 5162

South Asian (SAS) AF: 0.824 AC: 3963 AN: 4810

European-Finnish (FIN) AF: 0.677 AC: 7129 AN: 10528

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44231 AN: 67940

Other (OTH) AF: 0.721 AC: 1521 AN: 2110

Alfa AF: 0.677 Hom.: 14419

Bravo AF: 0.746

Asia WGS AF: 0.878 AC: 3050 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.73
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4380767; hg19: chr6-132946722; COSMIC: COSV63393403;