rs1960350

chr11-41728960-C-T

Variant summary

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

The NR_120584.1(LINC01499):n.37-5712C>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 0.226 in 152,096 control chromosomes in the GnomAD database, including 4,162 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 0.23 (4162 hom., cov: 33)
• Consequence: LINC01499 NR_120584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

LINC01499 (HGNC:51165): (long intergenic non-protein coding RNA 1499)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01499	NR_120584.1	n.37-5712C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01499	ENST00000648000.1	n.71-5712C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34372 AN: 151978 Hom.: 4159 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.226 AC: 34411 AN: 152096 Hom.: 4162 Cov.: 33 AF XY: 0.226 AC XY: 16822 AN XY: 74360

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.256

Alfa AF: 0.221 Hom.: 3548

Bravo AF: 0.241

Asia WGS AF: 0.343 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	5.7
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1960350; hg19: chr11-41750510;