rs13046799

chr21-30066838-T-Achr21-30066838-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;