9-103219790-A-G

Variant names:

• chr9-103219790-A-G
• rs10521064
• ENST00000411575.5:n.870+7924T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000411575.5(LINC01492):​n.870+7924T>C variant causes a intron 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 ENST00000411575.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411575.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01492	NR_121578.1		n.869+7924T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01492	ENST00000411575.5	TSL:1	n.870+7924T>C		intron	N/A
	LINC01492	ENST00000425157.3	TSL:5	n.388+7924T>C		intron	N/A
	LINC01492	ENST00000806271.1		n.513+7924T>C		intron	N/A

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

African (AFR) AF: 0.0887 AC: 3687 AN: 41556

American (AMR) AF: 0.0834 AC: 1275 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3470

East Asian (EAS) AF: 0.129 AC: 666 AN: 5156

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4828

European-Finnish (FIN) AF: 0.00819 AC: 87 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0139 AC: 945 AN: 68036

Other (OTH) AF: 0.0346 AC: 73 AN: 2112

Alfa AF: 0.0299 Hom.: 60

Bravo AF: 0.0570

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.71
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10521064; hg19: chr9-105982072;