rs6058897

Variant names:

• chr20-32810299-A-C
• rs6058897

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 0.609 in 152,112 control chromosomes in the GnomAD database, including 29,748 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 0.61 (29748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.609 AC: 92614 AN: 151994 Hom.: 29709 Cov.: 33

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.609 AC: 92710 AN: 152112 Hom.: 29748 Cov.: 33 AF XY: 0.614 AC XY: 45629 AN XY: 74368

African (AFR) AF: 0.765 AC: 31746 AN: 41488

American (AMR) AF: 0.615 AC: 9399 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5134 AN: 5166

South Asian (SAS) AF: 0.697 AC: 3368 AN: 4830

European-Finnish (FIN) AF: 0.514 AC: 5438 AN: 10574

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33858 AN: 67988

Other (OTH) AF: 0.560 AC: 1181 AN: 2108

Alfa AF: 0.542 Hom.: 18464

Bravo AF: 0.625

Asia WGS AF: 0.843 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.34
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6058897; hg19: chr20-31398105;