rs562370

Variant names:

• chr2-136525449-C-A
• rs562370

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.500 AC: 20687 AN: 41354

American (AMR) AF: 0.236 AC: 3601 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1541 AN: 3466

East Asian (EAS) AF: 0.305 AC: 1576 AN: 5174

South Asian (SAS) AF: 0.355 AC: 1700 AN: 4784

European-Finnish (FIN) AF: 0.155 AC: 1632 AN: 10544

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12455 AN: 67908

Other (OTH) AF: 0.318 AC: 669 AN: 2106

Alfa AF: 0.249 Hom.: 11408

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs562370; hg19: chr2-137283019;