1-24143903-C-T

Position:

• chr1-24143903-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;