rs2592888

Variant names:

• chr1-159615783-A-G
• rs2592888

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 0.356 in 152,074 control chromosomes in the GnomAD database, including 13,727 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 0.36 (13727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 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: 0.356 AC: 54032 AN: 151956 Hom.: 13703 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.356 AC: 54109 AN: 152074 Hom.: 13727 Cov.: 32 AF XY: 0.348 AC XY: 25873 AN XY: 74356

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0524

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.307

Alfa AF: 0.282 Hom.: 1320

Bravo AF: 0.368

Asia WGS AF: 0.142 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2592888; hg19: chr1-159585573;