rs6058897

Variant names:

• chr20-32810299-A-C
• rs6058897

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 0.609 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.609 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

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.560

Alfa AF: 0.544 Hom.: 14187

Bravo AF: 0.625

Asia WGS AF: 0.843 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6058897; hg19: chr20-31398105;