2-136137938-A-G

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 0.462 in 151,836 control chromosomes in the GnomAD database, including 18,065 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 0.46 (18065 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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 (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.461 AC: 69982 AN: 151718 Hom.: 18033 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.462 AC: 70077 AN: 151836 Hom.: 18065 Cov.: 31 AF XY: 0.470 AC XY: 34910 AN XY: 74212

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.544

Alfa AF: 0.374 Hom.: 11682

Bravo AF: 0.486

Asia WGS AF: 0.719 AC: 2497 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	1.3
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4954564; hg19: chr2-136895508;