rs2592889

Variant names:

• chr1-159614475-C-T
• rs2592889

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.649 AC: 26896 AN: 41454

American (AMR) AF: 0.210 AC: 3211 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3466

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5182

South Asian (SAS) AF: 0.190 AC: 916 AN: 4828

European-Finnish (FIN) AF: 0.242 AC: 2550 AN: 10542

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.223 AC: 15192 AN: 67976

Other (OTH) AF: 0.287 AC: 606 AN: 2112

Alfa AF: 0.293 Hom.: 1799

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs2592889; hg19: chr1-159584265;