rs1992917

Positions:

• chr9-103227361-A-G

Variant summary

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

The NR_121578.1(LINC01492):​n.869+353T>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 0.437 in 151,768 control chromosomes in the GnomAD database, including 14,734 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 0.44 (14734 hom., cov: 32)
• Consequence: LINC01492 NR_121578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01492	NR_121578.1	n.869+353T>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+353T>C		intron_variant, non_coding_transcript_variant		1
LINC01492	ENST00000425157.2	n.388+353T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66354 AN: 151650 Hom.: 14727 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.437 AC: 66373 AN: 151768 Hom.: 14734 Cov.: 32 AF XY: 0.439 AC XY: 32596 AN XY: 74174

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.426

Alfa AF: 0.444 Hom.: 1871

Bravo AF: 0.434

Asia WGS AF: 0.376 AC: 1305 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1992917; hg19: chr9-105989643;