rs580595

chr6-83486032-A-Gchr6-83486032-A-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 0.825 in 152,080 control chromosomes in the GnomAD database, including 52,074 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 0.82 (52074 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125333 AN: 151962 Hom.: 52009 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.825 AC: 125458 AN: 152080 Hom.: 52074 Cov.: 31 AF XY: 0.828 AC XY: 61514 AN XY: 74332

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.795

Alfa AF: 0.811 Hom.: 5860

Bravo AF: 0.827

Asia WGS AF: 0.898 AC: 3123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.53
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs580595; hg19: chr6-84195751;