rs2673582

Positions:

• chr8-132507817-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.538 in 151,974 control chromosomes in the GnomAD database, including 22,449 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 0.54 (22449 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.132507817C>T		intergenic_region
LOC124902028	XR_007061116.1	n.*18G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81682 AN: 151856 Hom.: 22425 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.538 AC: 81735 AN: 151974 Hom.: 22449 Cov.: 32 AF XY: 0.536 AC XY: 39787 AN XY: 74270

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.523

Alfa AF: 0.551 Hom.: 2916

Bravo AF: 0.537

Asia WGS AF: 0.466 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2673582; hg19: chr8-133520064;