20-61050291-C-G

Variant names:

• chr20-61050291-C-G
• rs2064855

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 0.716 in 152,090 control chromosomes in the GnomAD database, including 39,070 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 0.72 (39070 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 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: 0.716 AC: 108866 AN: 151972 Hom.: 39028 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.716 AC: 108968 AN: 152090 Hom.: 39070 Cov.: 33 AF XY: 0.716 AC XY: 53210 AN XY: 74330

African (AFR) AF: 0.707 AC: 29322 AN: 41472

American (AMR) AF: 0.655 AC: 10010 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2590 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3735 AN: 5134

South Asian (SAS) AF: 0.740 AC: 3567 AN: 4818

European-Finnish (FIN) AF: 0.728 AC: 7715 AN: 10600

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.730 AC: 49661 AN: 67988

Other (OTH) AF: 0.689 AC: 1457 AN: 2114

Alfa AF: 0.723 Hom.: 4924

Bravo AF: 0.708

Asia WGS AF: 0.781 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2064855; hg19: chr20-59625347;