rs13038362

Variant names:

• chr20-16647268-A-C
• rs13038362

Your query was ambiguous. Multiple possible variants found:

• chr20-16647268-A-C
• chr20-16647268-A-G

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 0.14 in 152,228 control chromosomes in the GnomAD database, including 1,654 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 0.14 (1654 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 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: 0.140 AC: 21237 AN: 152108 Hom.: 1650 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.140 AC: 21255 AN: 152228 Hom.: 1654 Cov.: 33 AF XY: 0.143 AC XY: 10676 AN XY: 74430

African (AFR) AF: 0.172 AC: 7127 AN: 41536

American (AMR) AF: 0.164 AC: 2503 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5180

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4820

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10592

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7047 AN: 68018

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.120 Hom.: 3833

Bravo AF: 0.144

Asia WGS AF: 0.261 AC: 905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.47
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs13038362; hg19: chr20-16627913;