rs13046373

chr21-30688172-A-G

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 0.512 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.568

Alfa AF: 0.539 Hom.: 4053

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13046373; hg19: chr21-32060490;