rs9323032

Variant names:

• chr14-40598733-A-G
• rs9323032
• XR_943790.3:n.829+13630T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_943790.3(LOC105370466):​n.829+13630T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,518 control chromosomes in the GnomAD database, including 18,287 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 0.48 (18287 hom., cov: 31)
• Consequence: LOC105370466 XR_943790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 0 publications found

Genes affected

LOC105370466 (HGNC:):

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 = 0.655 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: 0.476 AC: 72064 AN: 151400 Hom.: 18265 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.476 AC: 72142 AN: 151518 Hom.: 18287 Cov.: 31 AF XY: 0.480 AC XY: 35507 AN XY: 74014

African (AFR) AF: 0.661 AC: 27358 AN: 41366

American (AMR) AF: 0.460 AC: 6998 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3464

East Asian (EAS) AF: 0.539 AC: 2775 AN: 5148

South Asian (SAS) AF: 0.512 AC: 2468 AN: 4816

European-Finnish (FIN) AF: 0.389 AC: 4072 AN: 10468

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25404 AN: 67734

Other (OTH) AF: 0.454 AC: 955 AN: 2104

Alfa AF: 0.432 Hom.: 1986

Bravo AF: 0.490

Asia WGS AF: 0.532 AC: 1822 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.85
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs9323032; hg19: chr14-41067938;