rs302923

Variant names:

• chr9-132697260-T-C
• rs302923

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 0.157 in 152,116 control chromosomes in the GnomAD database, including 3,841 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 0.16 (3841 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.157 AC: 23905 AN: 151998 Hom.: 3835 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0453

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.157 AC: 23947 AN: 152116 Hom.: 3841 Cov.: 33 AF XY: 0.154 AC XY: 11488 AN XY: 74382

African (AFR) AF: 0.411 AC: 17032 AN: 41420

American (AMR) AF: 0.135 AC: 2065 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3472

East Asian (EAS) AF: 0.117 AC: 608 AN: 5186

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4822

European-Finnish (FIN) AF: 0.0453 AC: 480 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3088 AN: 68018

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.0755 Hom.: 566

Bravo AF: 0.177

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.70
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs302923; hg19: chr9-135572647;