20-33959574-G-C

Variant names:

• chr20-33959574-G-C
• rs2377956

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 0.641 in 150,952 control chromosomes in the GnomAD database, including 31,722 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 0.64 (31722 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.825 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: 0.641 AC: 96743 AN: 150838 Hom.: 31692 Cov.: 28

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.641 AC: 96828 AN: 150952 Hom.: 31722 Cov.: 28 AF XY: 0.652 AC XY: 47971 AN XY: 73600

African (AFR) AF: 0.506 AC: 20780 AN: 41038

American (AMR) AF: 0.658 AC: 9931 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3470

East Asian (EAS) AF: 0.844 AC: 4296 AN: 5090

South Asian (SAS) AF: 0.846 AC: 4066 AN: 4804

European-Finnish (FIN) AF: 0.744 AC: 7608 AN: 10232

Middle Eastern (MID) AF: 0.771 AC: 222 AN: 288

European-Non Finnish (NFE) AF: 0.667 AC: 45303 AN: 67920

Other (OTH) AF: 0.682 AC: 1429 AN: 2096

Alfa AF: 0.642 Hom.: 3711

Bravo AF: 0.627

Asia WGS AF: 0.800 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.061
DANN	Benign	0.37
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2377956; hg19: chr20-32547380;