9-1823774-G-C

Variant names:

• chr9-1823774-G-C
• rs1015250
• XR_001746599.1:n.142+104862G>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+104862G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,920 control chromosomes in the GnomAD database, including 11,553 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 0.34 (11553 hom., cov: 32)
• Consequence: LOC105375951 XR_001746599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 14 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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: 0.337 AC: 51174 AN: 151802 Hom.: 11507 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.338 AC: 51289 AN: 151920 Hom.: 11553 Cov.: 32 AF XY: 0.338 AC XY: 25092 AN XY: 74250

African (AFR) AF: 0.633 AC: 26242 AN: 41434

American (AMR) AF: 0.240 AC: 3657 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2501 AN: 5156

South Asian (SAS) AF: 0.344 AC: 1656 AN: 4820

European-Finnish (FIN) AF: 0.223 AC: 2358 AN: 10558

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12857 AN: 67920

Other (OTH) AF: 0.320 AC: 672 AN: 2102

Alfa AF: 0.268 Hom.: 941

Bravo AF: 0.357

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.42
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1015250; hg19: chr9-1823774;