rs13018756

chr2-136250665-C-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 0.369 in 152,032 control chromosomes in the GnomAD database, including 14,491 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 0.37 (14491 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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: 0.370 AC: 56146 AN: 151914 Hom.: 14495 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.369 AC: 56133 AN: 152032 Hom.: 14491 Cov.: 32 AF XY: 0.362 AC XY: 26871 AN XY: 74302

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.270

Alfa AF: 0.466 Hom.: 5208

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.13
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13018756; hg19: chr2-137008235;