chr20-31431051-C-T

Position:

• chr20-31431051-C-T

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 0.583 in 149,546 control chromosomes in the GnomAD database, including 26,104 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 0.58 (26104 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.583 AC: 87074 AN: 149438 Hom.: 26089 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.583 AC: 87113 AN: 149546 Hom.: 26104 Cov.: 31 AF XY: 0.584 AC XY: 42571 AN XY: 72926

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.594

Alfa AF: 0.628 Hom.: 40385

Bravo AF: 0.567

Asia WGS AF: 0.698 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2180566; hg19: chr20-30018854;