rs13006511

Variant names:

• chr2-108422634-T-C
• rs13006511

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 0.0849 in 152,236 control chromosomes in the GnomAD database, including 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 0.085 (720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 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: 0.0851 AC: 12938 AN: 152118 Hom.: 721 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0849 AC: 12931 AN: 152236 Hom.: 720 Cov.: 32 AF XY: 0.0828 AC XY: 6166 AN XY: 74434

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.0906

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.101

Alfa AF: 0.112 Hom.: 506

Bravo AF: 0.0827

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13006511; hg19: chr2-109039090;