rs7558386

Variant names:

• chr2-226697423-A-G
• rs7558386

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 0.474 in 152,084 control chromosomes in the GnomAD database, including 18,467 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 0.47 (18467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 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: 0.474 AC: 72002 AN: 151966 Hom.: 18422 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.474 AC: 72107 AN: 152084 Hom.: 18467 Cov.: 32 AF XY: 0.474 AC XY: 35239 AN XY: 74338

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.447

Alfa AF: 0.394 Hom.: 10637

Bravo AF: 0.497

Asia WGS AF: 0.540 AC: 1872 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7558386; hg19: chr2-227562139;