rs11792752

Variant names:

• chr9-19472462-A-C
• rs11792752
• XR_007061431.1:n.399+1962A>C

Variant summary

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

The XR_007061431.1(LOC105375988):​n.399+1962A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,964 control chromosomes in the GnomAD database, including 8,224 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 0.32 (8224 hom., cov: 32)
• Consequence: LOC105375988 XR_007061431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 1 publications found

Genes affected

LOC105375988 (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 (EAS) allele frequency at 95% confidence interval = 0.454 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: 0.319 AC: 48424 AN: 151846 Hom.: 8205 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.319 AC: 48488 AN: 151964 Hom.: 8224 Cov.: 32 AF XY: 0.327 AC XY: 24313 AN XY: 74248

African (AFR) AF: 0.391 AC: 16198 AN: 41420

American (AMR) AF: 0.330 AC: 5041 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 775 AN: 3464

East Asian (EAS) AF: 0.469 AC: 2418 AN: 5152

South Asian (SAS) AF: 0.376 AC: 1813 AN: 4816

European-Finnish (FIN) AF: 0.407 AC: 4298 AN: 10558

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17252 AN: 67960

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.273 Hom.: 8808

Bravo AF: 0.317

Asia WGS AF: 0.438 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs11792752; hg19: chr9-19472460;