rs1659258

Variant names:

• chr2-88360069-A-G
• rs1659258

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 0.0849 in 152,224 control chromosomes in the GnomAD database, including 604 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 0.085 (604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 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: 0.0849 AC: 12908 AN: 152106 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0576

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.0682

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0849 AC: 12919 AN: 152224 Hom.: 604 Cov.: 32 AF XY: 0.0873 AC XY: 6500 AN XY: 74432

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.0679

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0740 Hom.: 456

Bravo AF: 0.0821

Asia WGS AF: 0.0700 AC: 243 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	1.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1659258; hg19: chr2-88659588;