chr20-50338887-T-C

Variant names:

• chr20-50338887-T-C
• rs913678

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.507 in 152,172 control chromosomes in the GnomAD database, including 23,656 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 0.51 (23656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 70 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 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: 0.507 AC: 77066 AN: 152054 Hom.: 23597 Cov.: 33

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.507 AC: 77187 AN: 152172 Hom.: 23656 Cov.: 33 AF XY: 0.508 AC XY: 37777 AN XY: 74376

African (AFR) AF: 0.859 AC: 35674 AN: 41540

American (AMR) AF: 0.499 AC: 7624 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1466 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3484 AN: 5164

South Asian (SAS) AF: 0.383 AC: 1847 AN: 4818

European-Finnish (FIN) AF: 0.360 AC: 3810 AN: 10590

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21913 AN: 67988

Other (OTH) AF: 0.514 AC: 1085 AN: 2110

Alfa AF: 0.391 Hom.: 33833

Bravo AF: 0.540

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs913678; hg19: chr20-48955424;