1-24143903-C-T

Variant names:

• chr1-24143903-C-T
• rs16829225

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 0.189 in 152,102 control chromosomes in the GnomAD database, including 3,142 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 0.19 (3142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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: 0.189 AC: 28791 AN: 151984 Hom.: 3139 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.189 AC: 28818 AN: 152102 Hom.: 3142 Cov.: 32 AF XY: 0.187 AC XY: 13892 AN XY: 74356

African (AFR) AF: 0.279 AC: 11571 AN: 41468

American (AMR) AF: 0.152 AC: 2325 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.200 AC: 963 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1437 AN: 10576

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11140 AN: 67982

Other (OTH) AF: 0.193 AC: 409 AN: 2114

Alfa AF: 0.103 Hom.: 222

Bravo AF: 0.191

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.78
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs16829225; hg19: chr1-24470393;