2-136187459-C-T

Position:

• chr2-136187459-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 0.443 in 152,120 control chromosomes in the GnomAD database, including 16,702 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 0.44 (16702 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67236 AN: 152002 Hom.: 16662 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.443 AC: 67337 AN: 152120 Hom.: 16702 Cov.: 33 AF XY: 0.452 AC XY: 33605 AN XY: 74372

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.524

Alfa AF: 0.375 Hom.: 5358

Bravo AF: 0.466

Asia WGS AF: 0.695 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
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: rs1123848; hg19: chr2-136945029;