rs209957

chr20-54104556-G-Achr20-54104556-G-Cchr20-54104556-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;