rs13014034

Variant names:

• chr2-41173636-G-A
• rs13014034

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 0.233 in 151,756 control chromosomes in the GnomAD database, including 4,313 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 0.23 (4313 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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: 0.233 AC: 35331 AN: 151638 Hom.: 4316 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.233 AC: 35342 AN: 151756 Hom.: 4313 Cov.: 31 AF XY: 0.231 AC XY: 17161 AN XY: 74150

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.203

Alfa AF: 0.246 Hom.: 2722

Bravo AF: 0.222

Asia WGS AF: 0.117 AC: 405 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.075
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13014034; hg19: chr2-41400776;