20-51161341-A-G

Variant names:

• chr20-51161341-A-G
• rs2143630

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 0.803 in 152,120 control chromosomes in the GnomAD database, including 49,479 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 0.80 (49479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121986 AN: 152002 Hom.: 49428 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.803 AC: 122093 AN: 152120 Hom.: 49479 Cov.: 32 AF XY: 0.797 AC XY: 59243 AN XY: 74370

African (AFR) AF: 0.925 AC: 38417 AN: 41524

American (AMR) AF: 0.743 AC: 11345 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3382 AN: 5154

South Asian (SAS) AF: 0.627 AC: 3023 AN: 4818

European-Finnish (FIN) AF: 0.756 AC: 7994 AN: 10576

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52469 AN: 67988

Other (OTH) AF: 0.784 AC: 1654 AN: 2110

Alfa AF: 0.778 Hom.: 11394

Bravo AF: 0.810

Asia WGS AF: 0.666 AC: 2318 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	1.1
DANN	Benign	0.50
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2143630; hg19: chr20-49777878;