rs16922670

chr9-103261938-T-C

Variant summary

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

The NR_121578.1(LINC01492):n.771+2586A>G 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 0.164 in 152,208 control chromosomes in the GnomAD database, including 2,351 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 0.16 (2351 hom., cov: 32)
• Consequence: LINC01492 NR_121578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01492	NR_121578.1	n.771+2586A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01492	ENST00000411575.5	n.772+2586A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25021 AN: 152090 Hom.: 2355 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.164 AC: 25016 AN: 152208 Hom.: 2351 Cov.: 32 AF XY: 0.170 AC XY: 12616 AN XY: 74404

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.168

Alfa AF: 0.150 Hom.: 3430

Bravo AF: 0.176

Asia WGS AF: 0.221 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.5
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16922670; hg19: chr9-106024220;