chr20-51865839-T-C

Variant names:

• chr20-51865839-T-C
• rs6063725

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 0.316 in 152,128 control chromosomes in the GnomAD database, including 9,246 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 0.32 (9246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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: 0.316 AC: 48092 AN: 152010 Hom.: 9247 Cov.: 32

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.316 AC: 48087 AN: 152128 Hom.: 9246 Cov.: 32 AF XY: 0.317 AC XY: 23538 AN XY: 74360

Gnomad4 AFR AF: 0.0931

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.356

Alfa AF: 0.396 Hom.: 24732

Bravo AF: 0.306

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6063725; hg19: chr20-50482378;