rs13046373

Variant names:

• chr21-30688172-A-G
• rs13046373

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 0.512 in 151,916 control chromosomes in the GnomAD database, including 20,720 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 0.51 (20720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.601 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: 0.512 AC: 77770 AN: 151798 Hom.: 20703 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.512 AC: 77826 AN: 151916 Hom.: 20720 Cov.: 32 AF XY: 0.510 AC XY: 37889 AN XY: 74248

African (AFR) AF: 0.383 AC: 15852 AN: 41420

American (AMR) AF: 0.612 AC: 9329 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2136 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1589 AN: 5160

South Asian (SAS) AF: 0.609 AC: 2931 AN: 4816

European-Finnish (FIN) AF: 0.490 AC: 5170 AN: 10542

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.572 AC: 38858 AN: 67946

Other (OTH) AF: 0.568 AC: 1199 AN: 2110

Alfa AF: 0.538 Hom.: 7873

Bravo AF: 0.515

Asia WGS AF: 0.499 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.70
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs13046373; hg19: chr21-32060490;