rs1993434

chr9-103272026-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.644+4005T>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 0.375 in 151,664 control chromosomes in the GnomAD database, including 11,240 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 0.37 (11240 hom., cov: 31)
• Consequence: LINC01492 NR_121578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01492	NR_121578.1	n.644+4005T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01492	ENST00000411575.5	n.645+4005T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56823 AN: 151546 Hom.: 11231 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.375 AC: 56862 AN: 151664 Hom.: 11240 Cov.: 31 AF XY: 0.372 AC XY: 27559 AN XY: 74076

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.370

Alfa AF: 0.418 Hom.: 2761

Bravo AF: 0.366

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.9
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993434; hg19: chr9-106034308;