rs4815957

Variant names:

• chr20-6983149-A-G
• rs4815957

Your query was ambiguous. Multiple possible variants found:

• chr20-6983149-A-G
• chr20-6983149-A-T

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 0.548 in 151,956 control chromosomes in the GnomAD database, including 25,624 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 0.55 (25624 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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: 0.548 AC: 83172 AN: 151838 Hom.: 25625 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.548 AC: 83201 AN: 151956 Hom.: 25624 Cov.: 33 AF XY: 0.556 AC XY: 41254 AN XY: 74254

African (AFR) AF: 0.246 AC: 10194 AN: 41460

American (AMR) AF: 0.640 AC: 9735 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2098 AN: 3464

East Asian (EAS) AF: 0.786 AC: 4062 AN: 5168

South Asian (SAS) AF: 0.619 AC: 2983 AN: 4816

European-Finnish (FIN) AF: 0.728 AC: 7683 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44441 AN: 67968

Other (OTH) AF: 0.548 AC: 1156 AN: 2108

Alfa AF: 0.573 Hom.: 3478

Bravo AF: 0.527

Asia WGS AF: 0.661 AC: 2295 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs4815957; hg19: chr20-6963796;