rs9430161

Variant names:

• chr1-10986798-G-T
• rs9430161

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 0.268 in 151,996 control chromosomes in the GnomAD database, including 6,761 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 0.27 (6761 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 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: 0.268 AC: 40674 AN: 151878 Hom.: 6738 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.268 AC: 40734 AN: 151996 Hom.: 6761 Cov.: 31 AF XY: 0.264 AC XY: 19640 AN XY: 74304

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0776

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.257

Alfa AF: 0.210 Hom.: 7345

Bravo AF: 0.274

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.12
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9430161; hg19: chr1-11046855;