2-136349177-T-C

Position:

• chr2-136349177-T-C

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 0.633 in 151,992 control chromosomes in the GnomAD database, including 30,988 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 0.63 (30988 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 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: 0.633 AC: 96179 AN: 151872 Hom.: 30968 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.633 AC: 96233 AN: 151992 Hom.: 30988 Cov.: 31 AF XY: 0.632 AC XY: 46946 AN XY: 74296

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.660

Alfa AF: 0.547 Hom.: 1686

Bravo AF: 0.621

Asia WGS AF: 0.629 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
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: rs4501004; hg19: chr2-137106747;