rs2151499

Positions:

• chr13-22655014-G-A

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 0.144 in 152,200 control chromosomes in the GnomAD database, including 1,922 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 0.14 (1922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 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: 0.144 AC: 21954 AN: 152084 Hom.: 1921 Cov.: 33

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.144 AC: 21957 AN: 152200 Hom.: 1922 Cov.: 33 AF XY: 0.150 AC XY: 11191 AN XY: 74400

Gnomad4 AFR AF: 0.0615

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.142

Alfa AF: 0.144 Hom.: 264

Bravo AF: 0.127

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2151499; hg19: chr13-23229153;