chr2-136059518-C-T

Position:

• chr2-136059518-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 0.407 in 151,502 control chromosomes in the GnomAD database, including 17,578 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 0.41 (17578 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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: 0.408 AC: 61692 AN: 151386 Hom.: 17582 Cov.: 30

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.407 AC: 61683 AN: 151502 Hom.: 17578 Cov.: 30 AF XY: 0.395 AC XY: 29261 AN XY: 74012

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0287

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.317

Alfa AF: 0.533 Hom.: 33014

Bravo AF: 0.369

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs749873; hg19: chr2-136817088;