rs1558626

chr2-102245610-T-Achr2-102245610-T-Cchr2-102245610-T-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 0.338 in 151,870 control chromosomes in the GnomAD database, including 9,558 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 0.34 (9558 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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: 0.338 AC: 51299 AN: 151752 Hom.: 9565 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.338 AC: 51303 AN: 151870 Hom.: 9558 Cov.: 31 AF XY: 0.346 AC XY: 25643 AN XY: 74204

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.335

Alfa AF: 0.233 Hom.: 588

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.63
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558626; hg19: chr2-102862070;