rs9427092

chr1-154581246-T-C

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 0.169 in 152,228 control chromosomes in the GnomAD database, including 2,506 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 (2506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

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 (SAS) allele frequency at 95% confidence interval = 0.233 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: 0.169 AC: 25776 AN: 152110 Hom.: 2505 Cov.: 32

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.169 AC: 25774 AN: 152228 Hom.: 2506 Cov.: 32 AF XY: 0.173 AC XY: 12913 AN XY: 74432

Gnomad4 AFR AF: 0.0852

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.161

Alfa AF: 0.191 Hom.: 971

Bravo AF: 0.157

Asia WGS AF: 0.241 AC: 837 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	0.86
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9427092; hg19: chr1-154553722;