rs1558626

Variant names:

• chr2-102245610-T-A
• rs1558626

Your query was ambiguous. Multiple possible variants found:

• chr2-102245610-T-A
• chr2-102245610-T-C
• chr2-102245610-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;