20-51161341-A-G

Variant names:

• chr20-51161341-A-G
• rs2143630

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 0.803 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.803 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

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.784

Alfa AF: 0.775 Hom.: 11059

Bravo AF: 0.810

Asia WGS AF: 0.666 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143630; hg19: chr20-49777878;