rs272594

Variant names:

• chr8-80557885-A-C
• rs272594

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 0.211 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

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.200

Alfa AF: 0.143 Hom.: 3275

Bravo AF: 0.218

Asia WGS AF: 0.147 AC: 510 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs272594; hg19: chr8-81470120;