rs13046799

Variant names:

• chr21-30066838-T-A
• rs13046799

Your query was ambiguous. Multiple possible variants found:

• chr21-30066838-T-A
• chr21-30066838-T-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 0.179 in 152,142 control chromosomes in the GnomAD database, including 2,883 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 (2883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 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: 0.179 AC: 27141 AN: 152024 Hom.: 2879 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.0646

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.179 AC: 27159 AN: 152142 Hom.: 2883 Cov.: 32 AF XY: 0.175 AC XY: 13027 AN XY: 74404

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.0646

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.169

Alfa AF: 0.0587 Hom.: 53

Bravo AF: 0.185

Asia WGS AF: 0.236 AC: 814 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13046799; hg19: chr21-31439156;