rs9430161

Variant names:

• chr1-10986798-G-T
• rs9430161

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 0.268 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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.462 AC: 19127 AN: 41424

American (AMR) AF: 0.174 AC: 2658 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3472

East Asian (EAS) AF: 0.0776 AC: 402 AN: 5178

South Asian (SAS) AF: 0.106 AC: 514 AN: 4828

European-Finnish (FIN) AF: 0.243 AC: 2569 AN: 10552

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13760 AN: 67978

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.219 Hom.: 17553

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs9430161; hg19: chr1-11046855;