20-38345596-A-T

Variant names:

• chr20-38345596-A-T
• rs5741812

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 0.181 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.280 AC: 11596 AN: 41372

American (AMR) AF: 0.136 AC: 2082 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2330 AN: 5174

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4820

European-Finnish (FIN) AF: 0.0812 AC: 858 AN: 10564

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8437 AN: 67966

Other (OTH) AF: 0.169 AC: 357 AN: 2112

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs5741812; hg19: chr20-36973999;