rs742393

Variant names:

• chr1-25199390-G-A
• rs742393

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 0.168 in 152,162 control chromosomes in the GnomAD database, including 2,179 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 0.17 (2179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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: 0.168 AC: 25499 AN: 152044 Hom.: 2177 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.168 AC: 25507 AN: 152162 Hom.: 2179 Cov.: 32 AF XY: 0.168 AC XY: 12520 AN XY: 74392

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.168

Alfa AF: 0.177 Hom.: 3096

Bravo AF: 0.166

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs742393; hg19: chr1-25525881;