20-51943113-T-C

Position:

• chr20-51943113-T-C

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 0.631 in 152,022 control chromosomes in the GnomAD database, including 30,371 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 0.63 (30371 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95909 AN: 151904 Hom.: 30342 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.631 AC: 95977 AN: 152022 Hom.: 30371 Cov.: 33 AF XY: 0.631 AC XY: 46846 AN XY: 74296

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.655

Alfa AF: 0.643 Hom.: 71511

Bravo AF: 0.635

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6068020; hg19: chr20-50559652;