rs272594

Variant names:

• chr8-80557885-A-C
• rs272594

Variant summary

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

The variant allele was found at a frequency of 0.211 in 151,974 control chromosomes in the GnomAD database, including 4,445 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 0.21 (4445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31948 AN: 151856 Hom.: 4425 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.211 AC: 32017 AN: 151974 Hom.: 4445 Cov.: 32 AF XY: 0.205 AC XY: 15255 AN XY: 74284

African (AFR) AF: 0.402 AC: 16638 AN: 41406

American (AMR) AF: 0.152 AC: 2321 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3468

East Asian (EAS) AF: 0.121 AC: 627 AN: 5176

South Asian (SAS) AF: 0.155 AC: 744 AN: 4812

European-Finnish (FIN) AF: 0.121 AC: 1275 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9423 AN: 67966

Other (OTH) AF: 0.200 AC: 423 AN: 2110

Alfa AF: 0.158 Hom.: 9326

Bravo AF: 0.218

Asia WGS AF: 0.147 AC: 510 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs272594; hg19: chr8-81470120;