rs396250

Positions:

• chr9-103325054-G-A
• chr9-103325054-G-C

Variant summary

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

The 9-103325054-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,188 control chromosomes in the GnomAD database, including 665 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 0.086 (665 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01492 NR_121578.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966

Genes affected

LINC01492 (HGNC:51149): (long intergenic non-protein coding RNA 1492)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01492	NR_121578.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01492	ENST00000411575.5			upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0864 AC: 13142 AN: 152070 Hom.: 665 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.110

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0863 AC: 13135 AN: 152188 Hom.: 665 Cov.: 32 AF XY: 0.0849 AC XY: 6318 AN XY: 74402

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0155

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0904 Hom.: 75

Bravo AF: 0.0872

Asia WGS AF: 0.0530 AC: 182 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	4.8
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs396250; hg19: chr9-106087336;