20-32811837-T-C

Variant names:

• chr20-32811837-T-C
• rs406193

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 0.913 in 152,296 control chromosomes in the GnomAD database, including 63,679 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 0.91 (63679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.913 AC: 138986 AN: 152178 Hom.: 63618 Cov.: 32

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.913 AC: 139107 AN: 152296 Hom.: 63679 Cov.: 32 AF XY: 0.916 AC XY: 68206 AN XY: 74460

African (AFR) AF: 0.977 AC: 40599 AN: 41572

American (AMR) AF: 0.902 AC: 13796 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3105 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5176 AN: 5190

South Asian (SAS) AF: 0.930 AC: 4491 AN: 4828

European-Finnish (FIN) AF: 0.913 AC: 9682 AN: 10602

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59244 AN: 68016

Other (OTH) AF: 0.893 AC: 1889 AN: 2116

Alfa AF: 0.895 Hom.: 53100

Bravo AF: 0.914

Asia WGS AF: 0.964 AC: 3350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.42
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs406193; hg19: chr20-31399643;