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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375951	XR_001746599.1	n.142+74603G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;