20-50404983-T-C

Variant names:

• chr20-50404983-T-C
• rs6512631

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 0.754 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6512631; hg19: chr20-49021520;