rs7566637

Variant names:

• chr2-10282813-C-T
• rs7566637

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 0.213 in 152,198 control chromosomes in the GnomAD database, including 4,032 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 0.21 (4032 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.213 AC: 32399 AN: 152080 Hom.: 4010 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0833

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.213 AC: 32461 AN: 152198 Hom.: 4032 Cov.: 33 AF XY: 0.214 AC XY: 15922 AN XY: 74422

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0837

Gnomad4 SAS AF: 0.0888

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.191

Alfa AF: 0.189 Hom.: 1347

Bravo AF: 0.212

Asia WGS AF: 0.0970 AC: 338 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	0.053
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7566637; hg19: chr2-10422939;