rs9290128

Variant names:

• chr3-162592591-A-C
• rs9290128

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 0.174 in 151,798 control chromosomes in the GnomAD database, including 2,664 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 (2664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 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: 0.175 AC: 26471 AN: 151680 Hom.: 2663 Cov.: 32

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.174 AC: 26483 AN: 151798 Hom.: 2664 Cov.: 32 AF XY: 0.171 AC XY: 12700 AN XY: 74204

African (AFR) AF: 0.0976 AC: 4050 AN: 41504

American (AMR) AF: 0.128 AC: 1948 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3466

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5178

South Asian (SAS) AF: 0.182 AC: 878 AN: 4824

European-Finnish (FIN) AF: 0.207 AC: 2188 AN: 10566

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.240 AC: 16258 AN: 67700

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.222 Hom.: 2028

Bravo AF: 0.163

Asia WGS AF: 0.100 AC: 349 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.40
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9290128; hg19: chr3-162310379;