rs9290105

Variant names:

• chr3-161957236-A-G
• rs9290105

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 0.0852 in 152,128 control chromosomes in the GnomAD database, including 782 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 0.085 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0853 AC: 12961 AN: 152010 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0852 AC: 12958 AN: 152128 Hom.: 782 Cov.: 32 AF XY: 0.0847 AC XY: 6303 AN XY: 74378

African (AFR) AF: 0.0234 AC: 973 AN: 41546

American (AMR) AF: 0.0515 AC: 787 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3464

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5188

South Asian (SAS) AF: 0.0674 AC: 325 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10588

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8899 AN: 67912

Other (OTH) AF: 0.0649 AC: 137 AN: 2110

Alfa AF: 0.110 Hom.: 140

Bravo AF: 0.0726

Asia WGS AF: 0.0330 AC: 115 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs9290105; hg19: chr3-161675024;