chr20-50404983-T-C

Variant names:

• chr20-50404983-T-C
• rs6512631

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 0.754 in 152,172 control chromosomes in the GnomAD database, including 43,473 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 0.75 (43473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.8 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: 0.754 AC: 114713 AN: 152054 Hom.: 43441 Cov.: 33

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.754 AC: 114795 AN: 152172 Hom.: 43473 Cov.: 33 AF XY: 0.757 AC XY: 56322 AN XY: 74392

African (AFR) AF: 0.726 AC: 30131 AN: 41494

American (AMR) AF: 0.812 AC: 12422 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2531 AN: 3472

East Asian (EAS) AF: 0.581 AC: 2998 AN: 5160

South Asian (SAS) AF: 0.785 AC: 3792 AN: 4828

European-Finnish (FIN) AF: 0.822 AC: 8713 AN: 10594

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51791 AN: 68010

Other (OTH) AF: 0.737 AC: 1557 AN: 2112

Alfa AF: 0.716 Hom.: 3542

Bravo AF: 0.752

Asia WGS AF: 0.681 AC: 2370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.53
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6512631; hg19: chr20-49021520;