2-136061149-C-T

Variant names:

• chr2-136061149-C-T
• rs2090660

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 0.247 in 152,064 control chromosomes in the GnomAD database, including 5,652 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 0.25 (5652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 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: 0.248 AC: 37609 AN: 151946 Hom.: 5648 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.247 AC: 37617 AN: 152064 Hom.: 5652 Cov.: 32 AF XY: 0.255 AC XY: 18930 AN XY: 74332

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.344

Alfa AF: 0.260 Hom.: 3984

Bravo AF: 0.253

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	7.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2090660; hg19: chr2-136818719;