chr20-50433551-C-G

Variant names:

• chr20-50433551-C-G
• rs2904268

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 0.65 in 151,948 control chromosomes in the GnomAD database, including 32,720 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 0.65 (32720 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.767 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: 0.651 AC: 98769 AN: 151830 Hom.: 32729 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.650 AC: 98787 AN: 151948 Hom.: 32720 Cov.: 31 AF XY: 0.658 AC XY: 48847 AN XY: 74254

African (AFR) AF: 0.535 AC: 22180 AN: 41422

American (AMR) AF: 0.755 AC: 11528 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2435 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2763 AN: 5156

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4822

European-Finnish (FIN) AF: 0.758 AC: 8003 AN: 10552

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45953 AN: 67938

Other (OTH) AF: 0.641 AC: 1350 AN: 2106

Alfa AF: 0.545 Hom.: 1545

Bravo AF: 0.645

Asia WGS AF: 0.638 AC: 2221 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	1.6
DANN	Benign	0.29
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2904268; hg19: chr20-49050088;