2-137867784-C-T

Position:

• chr2-137867784-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 0.387 in 151,100 control chromosomes in the GnomAD database, including 12,065 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 0.39 (12065 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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: 0.388 AC: 58516 AN: 150984 Hom.: 12070 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.387 AC: 58500 AN: 151100 Hom.: 12065 Cov.: 31 AF XY: 0.391 AC XY: 28880 AN XY: 73790

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.434

Alfa AF: 0.392 Hom.: 2059

Bravo AF: 0.377

Asia WGS AF: 0.542 AC: 1878 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10460245; hg19: chr2-138625354;