rs1015250

Variant names:

• chr9-1823774-G-C
• rs1015250
• XR_001746599.1:n.142+104862G>C

Your query was ambiguous. Multiple possible variants found:

• chr9-1823774-G-C
• chr9-1823774-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375951	XR_001746599.1	n.142+104862G>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.337 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 v4.3

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;