rs2592889

Positions:

• chr1-159614475-C-T

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 0.333 in 152,050 control chromosomes in the GnomAD database, including 11,494 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 0.33 (11494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

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 = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50583 AN: 151932 Hom.: 11474 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.333 AC: 50653 AN: 152050 Hom.: 11494 Cov.: 32 AF XY: 0.326 AC XY: 24204 AN XY: 74308

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.287

Alfa AF: 0.284 Hom.: 1630

Bravo AF: 0.343

Asia WGS AF: 0.139 AC: 487 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	1.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2592889; hg19: chr1-159584265;