rs10521064

Positions:

• chr9-103219790-A-G
• chr9-103219790-A-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+7924T>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 0.0447 in 152,274 control chromosomes in the GnomAD database, including 299 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 (299 hom., cov: 32)
• Consequence: LINC01492 NR_121578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01492	NR_121578.1	n.869+7924T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01492	ENST00000411575.5	n.870+7924T>C		intron_variant, non_coding_transcript_variant		1
LINC01492	ENST00000425157.2	n.388+7924T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0447 AC: 6797 AN: 152156 Hom.: 299 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0139

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0447 AC: 6814 AN: 152274 Hom.: 299 Cov.: 32 AF XY: 0.0443 AC XY: 3295 AN XY: 74460

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.0834

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.00819

Gnomad4 NFE AF: 0.0139

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0308 Hom.: 33

Bravo AF: 0.0570

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521064; hg19: chr9-105982072;