rs13043694

Variant names:

• chr20-48459908-G-A
• rs13043694

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 0.293 in 151,838 control chromosomes in the GnomAD database, including 6,816 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 0.29 (6816 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 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: 0.293 AC: 44410 AN: 151720 Hom.: 6804 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.293 AC: 44437 AN: 151838 Hom.: 6816 Cov.: 31 AF XY: 0.299 AC XY: 22158 AN XY: 74166

African (AFR) AF: 0.244 AC: 10092 AN: 41364

American (AMR) AF: 0.426 AC: 6495 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3470

East Asian (EAS) AF: 0.339 AC: 1743 AN: 5140

South Asian (SAS) AF: 0.332 AC: 1603 AN: 4822

European-Finnish (FIN) AF: 0.332 AC: 3482 AN: 10500

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19180 AN: 67974

Other (OTH) AF: 0.282 AC: 597 AN: 2116

Alfa AF: 0.280 Hom.: 2170

Bravo AF: 0.298

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs13043694; hg19: chr20-47088154;