rs209957

Variant names:

• chr20-54104556-G-A
• rs209957

Your query was ambiguous. Multiple possible variants found:

• chr20-54104556-G-A
• chr20-54104556-G-C
• chr20-54104556-G-T

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 0.762 in 152,150 control chromosomes in the GnomAD database, including 44,682 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 0.76 (44682 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.762 AC: 115801 AN: 152032 Hom.: 44622 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.762 AC: 115918 AN: 152150 Hom.: 44682 Cov.: 32 AF XY: 0.762 AC XY: 56676 AN XY: 74368

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.720

Alfa AF: 0.714 Hom.: 53006

Bravo AF: 0.754

Asia WGS AF: 0.866 AC: 3013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs209957; hg19: chr20-52721095;