rs13014034

chr2-41173636-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;