rs9427092

Variant names:

• chr1-154581246-T-C
• rs9427092

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 0.169 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
• Publications: 16 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 (SAS) allele frequency at 95% confidence interval = 0.233 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: 0.169 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

African (AFR) AF: 0.0852 AC: 3537 AN: 41538

American (AMR) AF: 0.149 AC: 2279 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1155 AN: 5170

South Asian (SAS) AF: 0.245 AC: 1181 AN: 4830

European-Finnish (FIN) AF: 0.241 AC: 2550 AN: 10592

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13708 AN: 68012

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.192 Hom.: 2093

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
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs9427092; hg19: chr1-154553722;