rs3007246

Variant names:

• chr13-105169695-C-T
• rs3007246

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 0.0672 in 152,070 control chromosomes in the GnomAD database, including 528 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 0.067 (528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 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: 0.0671 AC: 10196 AN: 151952 Hom.: 526 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.00566

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0672 AC: 10217 AN: 152070 Hom.: 528 Cov.: 32 AF XY: 0.0659 AC XY: 4901 AN XY: 74330

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0920

Gnomad4 ASJ AF: 0.0475

Gnomad4 EAS AF: 0.0627

Gnomad4 SAS AF: 0.0294

Gnomad4 FIN AF: 0.00566

Gnomad4 NFE AF: 0.0332

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0442 Hom.: 299

Bravo AF: 0.0767

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3007246; hg19: chr13-105822046;