chr2-136525449-C-A

Variant names:

• chr2-136525449-C-A
• rs562370

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 0.29 in 151,798 control chromosomes in the GnomAD database, including 8,019 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 0.29 (8019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.290 AC: 43978 AN: 151680 Hom.: 7988 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.290 AC: 44064 AN: 151798 Hom.: 8019 Cov.: 32 AF XY: 0.291 AC XY: 21560 AN XY: 74176

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.318

Alfa AF: 0.225 Hom.: 6263

Bravo AF: 0.302

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	14
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs562370; hg19: chr2-137283019;