rs2125000

Variant names:

• chr4-124344158-C-T
• rs2125000

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 0.218 in 151,906 control chromosomes in the GnomAD database, including 4,406 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 0.22 (4406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33143 AN: 151786 Hom.: 4406 Cov.: 32

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.218 AC: 33147 AN: 151906 Hom.: 4406 Cov.: 32 AF XY: 0.220 AC XY: 16341 AN XY: 74234

African (AFR) AF: 0.0654 AC: 2713 AN: 41492

American (AMR) AF: 0.280 AC: 4275 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1288 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1536 AN: 5158

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4814

European-Finnish (FIN) AF: 0.260 AC: 2738 AN: 10544

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18621 AN: 67864

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.259 Hom.: 18228

Bravo AF: 0.211

Asia WGS AF: 0.263 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.73
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2125000; hg19: chr4-125265313;