20-38345596-A-T

Position:

• chr20-38345596-A-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 0.181 in 151,960 control chromosomes in the GnomAD database, including 3,140 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 0.18 (3140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27472 AN: 151842 Hom.: 3139 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.181 AC: 27491 AN: 151960 Hom.: 3140 Cov.: 32 AF XY: 0.182 AC XY: 13546 AN XY: 74292

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0812

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.169

Alfa AF: 0.151 Hom.: 269

Bravo AF: 0.186

Asia WGS AF: 0.300 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5741812; hg19: chr20-36973999;