9-1793515-G-C

Variant names:

• chr9-1793515-G-C
• rs10511431
• XR_001746599.1:n.142+74603G>C

Variant summary

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

The XR_001746599.1(LOC105375951):​n.142+74603G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,074 control chromosomes in the GnomAD database, including 14,716 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 0.43 (14716 hom., cov: 33)
• Consequence: LOC105375951 XR_001746599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 2 publications found

Genes affected

LOC105375951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 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: 0.426 AC: 64659 AN: 151954 Hom.: 14698 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.425 AC: 64704 AN: 152074 Hom.: 14716 Cov.: 33 AF XY: 0.429 AC XY: 31913 AN XY: 74332

African (AFR) AF: 0.256 AC: 10601 AN: 41484

American (AMR) AF: 0.423 AC: 6468 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2786 AN: 5174

South Asian (SAS) AF: 0.483 AC: 2324 AN: 4810

European-Finnish (FIN) AF: 0.539 AC: 5689 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33769 AN: 67978

Other (OTH) AF: 0.436 AC: 918 AN: 2104

Alfa AF: 0.313 Hom.: 834

Bravo AF: 0.408

Asia WGS AF: 0.486 AC: 1690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.67
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10511431; hg19: chr9-1793515; COSMIC: COSV69442178;