rs13006559

Variant names:

• chr2-102291170-T-C
• rs13006559

Your query was ambiguous. Multiple possible variants found:

• chr2-102291170-T-C
• chr2-102291170-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 0.668 in 151,946 control chromosomes in the GnomAD database, including 34,403 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 0.67 (34403 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16

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 (EAS) allele frequency at 95% confidence interval = 0.95 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: 0.668 AC: 101447 AN: 151828 Hom.: 34369 Cov.: 30

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.668 AC: 101531 AN: 151946 Hom.: 34403 Cov.: 30 AF XY: 0.676 AC XY: 50174 AN XY: 74272

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.668

Alfa AF: 0.624 Hom.: 4298

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.068
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13006559; hg19: chr2-102907630;