chr2-137727463-G-A

Position:

• chr2-137727463-G-A

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 0.157 in 135,116 control chromosomes in the GnomAD database, including 2,889 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 0.16 (2889 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.157 AC: 21204 AN: 134988 Hom.: 2872 Cov.: 30

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.157 AC: 21266 AN: 135116 Hom.: 2889 Cov.: 30 AF XY: 0.160 AC XY: 10634 AN XY: 66572

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0289

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0827 Hom.: 183

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446224; hg19: chr2-138485033;