rs1448576

Positions:

• chr9-103221395-G-A
• chr9-103221395-G-C
• chr9-103221395-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+6319C>T 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 0.429 in 151,794 control chromosomes in the GnomAD database, including 14,263 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 0.43 (14263 hom., cov: 31)
• Consequence: LINC01492 NR_121578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01492	NR_121578.1	n.869+6319C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01492	ENST00000411575.5	n.870+6319C>T		intron_variant, non_coding_transcript_variant		1
LINC01492	ENST00000425157.2	n.388+6319C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65166 AN: 151676 Hom.: 14258 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.429 AC: 65183 AN: 151794 Hom.: 14263 Cov.: 31 AF XY: 0.432 AC XY: 32042 AN XY: 74154

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.419

Alfa AF: 0.366 Hom.: 1538

Bravo AF: 0.425

Asia WGS AF: 0.376 AC: 1304 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448576; hg19: chr9-105983677;