1-24143903-C-T

Variant names:

• chr1-24143903-C-T
• rs16829225

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 0.189 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.189 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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.193

Alfa AF: 0.0964 Hom.: 197

Bravo AF: 0.191

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16829225; hg19: chr1-24470393;