chr20-32811837-T-C

Position:

• chr20-32811837-T-C

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 0.913 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.977

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.893

Alfa AF: 0.888 Hom.: 24764

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs406193; hg19: chr20-31399643;