9-90646879-T-G

Variant names:

• chr9-90646879-T-G
• rs1412005

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 0.682 in 152,128 control chromosomes in the GnomAD database, including 35,926 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 0.68 (35926 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103629 AN: 152010 Hom.: 35910 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.682 AC: 103697 AN: 152128 Hom.: 35926 Cov.: 33 AF XY: 0.679 AC XY: 50517 AN XY: 74358

African (AFR) AF: 0.595 AC: 24707 AN: 41508

American (AMR) AF: 0.626 AC: 9568 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2738 AN: 3472

East Asian (EAS) AF: 0.444 AC: 2288 AN: 5158

South Asian (SAS) AF: 0.792 AC: 3818 AN: 4822

European-Finnish (FIN) AF: 0.672 AC: 7108 AN: 10576

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51029 AN: 67984

Other (OTH) AF: 0.730 AC: 1542 AN: 2112

Alfa AF: 0.729 Hom.: 167211

Bravo AF: 0.671

Asia WGS AF: 0.618 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.1
DANN	Benign	0.51
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1412005; hg19: chr9-93409161;