rs1024125

Variant names:

• chr2-173843471-T-C
• rs1024125

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.726 in 152,084 control chromosomes in the GnomAD database, including 40,155 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 0.73 (40155 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110312 AN: 151966 Hom.: 40098 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.726 AC: 110428 AN: 152084 Hom.: 40155 Cov.: 31 AF XY: 0.732 AC XY: 54374 AN XY: 74326

African (AFR) AF: 0.739 AC: 30652 AN: 41470

American (AMR) AF: 0.775 AC: 11848 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3468

East Asian (EAS) AF: 0.799 AC: 4138 AN: 5180

South Asian (SAS) AF: 0.812 AC: 3905 AN: 4812

European-Finnish (FIN) AF: 0.722 AC: 7633 AN: 10570

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47142 AN: 67970

Other (OTH) AF: 0.731 AC: 1546 AN: 2114

Alfa AF: 0.710 Hom.: 66283

Bravo AF: 0.729

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	22
DANN	Benign	0.77
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs1024125; hg19: chr2-174708199;