rs13006511

Variant names:

• chr2-108422634-T-C
• rs13006511

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0216 AC: 897 AN: 41552

American (AMR) AF: 0.0906 AC: 1386 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0452 AC: 218 AN: 4820

European-Finnish (FIN) AF: 0.0752 AC: 798 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8721 AN: 67994

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.0977 Hom.: 700

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs13006511; hg19: chr2-109039090;