rs6065961

Variant names:

• chr20-46339617-C-A
• rs6065961

Your query was ambiguous. Multiple possible variants found:

• chr20-46339617-C-A
• chr20-46339617-C-G

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 0.0855 in 152,286 control chromosomes in the GnomAD database, including 763 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 0.085 (763 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.125 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: 0.0856 AC: 13024 AN: 152168 Hom.: 764 Cov.: 32

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0855 AC: 13016 AN: 152286 Hom.: 763 Cov.: 32 AF XY: 0.0845 AC XY: 6296 AN XY: 74474

African (AFR) AF: 0.0219 AC: 908 AN: 41556

American (AMR) AF: 0.0581 AC: 889 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3468

East Asian (EAS) AF: 0.00849 AC: 44 AN: 5182

South Asian (SAS) AF: 0.118 AC: 571 AN: 4828

European-Finnish (FIN) AF: 0.136 AC: 1446 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8661 AN: 68016

Other (OTH) AF: 0.0638 AC: 135 AN: 2116

Alfa AF: 0.0889 Hom.: 628

Bravo AF: 0.0757

Asia WGS AF: 0.0550 AC: 191 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	0.32
DANN	Benign	0.42
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6065961; hg19: chr20-44968255;