rs2125000

Variant names:

• chr4-124344158-C-T
• rs2125000

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 0.218 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.218 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

Gnomad4 AFR AF: 0.0654

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.232

Alfa AF: 0.271 Hom.: 12175

Bravo AF: 0.211

Asia WGS AF: 0.263 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2125000; hg19: chr4-125265313;