rs1015250

chr9-1823774-G-Cchr9-1823774-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746599.1(LOC105375951):n.142+104862G>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

Genes affected

LOC105375951 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375951	XR_001746599.1	n.142+104862G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.320

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015250; hg19: chr9-1823774;