chr20-46339617-C-A

Variant names:

• chr20-46339617-C-A
• rs6065961

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 0.0855 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

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 (NFE) allele frequency at 95% confidence interval = 0.125 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: 0.0856 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

Gnomad4 AFR AF: 0.0219

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.00849

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0965 Hom.: 431

Bravo AF: 0.0757

Asia WGS AF: 0.0550 AC: 191 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	0.32
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6065961; hg19: chr20-44968255;