rs10521063

Positions:

• chr9-103218894-G-T

Variant summary

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

The NR_121578.1(LINC01492):​n.869+8820C>A 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 0.0449 in 152,106 control chromosomes in the GnomAD database, including 301 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 0.045 (301 hom., cov: 33)
• Consequence: LINC01492 NR_121578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01492	NR_121578.1	n.869+8820C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01492	ENST00000411575.5	n.870+8820C>A		intron_variant, non_coding_transcript_variant		1
LINC01492	ENST00000425157.2	n.388+8820C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6811 AN: 151986 Hom.: 301 Cov.: 33

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.00833

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0139

Gnomad OTH AF: 0.0350

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

GnomAD4 genome AF: 0.0449 AC: 6828 AN: 152106 Hom.: 301 Cov.: 33 AF XY: 0.0444 AC XY: 3301 AN XY: 74354

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.0835

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.00833

Gnomad4 NFE AF: 0.0139

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0327 Hom.: 27

Bravo AF: 0.0569

Asia WGS AF: 0.0660 AC: 228 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521063; hg19: chr9-105981176;