rs11113894

Positions:

• chr12-108448086-G-A

Variant summary

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

The ENST00000502160.6(LINC01498):​n.2447+300C>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 0.141 in 152,090 control chromosomes in the GnomAD database, including 2,372 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 0.14 (2372 hom., cov: 32)
• Consequence: LINC01498 ENST00000502160.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

LINC01498 (HGNC:51164): (long intergenic non-protein coding RNA 1498)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01498	ENST00000502160.6	n.2447+300C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21408 AN: 151972 Hom.: 2362 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.141 AC: 21458 AN: 152090 Hom.: 2372 Cov.: 32 AF XY: 0.149 AC XY: 11094 AN XY: 74348

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0971 Hom.: 1223

Bravo AF: 0.162

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11113894; hg19: chr12-108841863;