rs12613304

chr2-58340157-G-Achr2-58340157-G-Cchr2-58340157-G-T

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 0.171 in 152,070 control chromosomes in the GnomAD database, including 2,402 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 0.17 (2402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 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: 0.171 AC: 25941 AN: 151950 Hom.: 2403 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.171 AC: 25951 AN: 152070 Hom.: 2402 Cov.: 32 AF XY: 0.172 AC XY: 12772 AN XY: 74316

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.206

Alfa AF: 0.113 Hom.: 211

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.085
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12613304; hg19: chr2-58567292;