rs4815957

chr20-6983149-A-Gchr20-6983149-A-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 0.548 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.548

Alfa AF: 0.587 Hom.: 3457

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815957; hg19: chr20-6963796;