rs9430161

Positions:

• chr1-10986798-G-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 0.268 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;