rs6058897

Positions:

• chr20-32810299-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;