ENST00000502160.6:n.206+2409G>A

Variant names:

• chr12-108483764-C-T
• rs918304
• ENST00000502160.6:n.206+2409G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502160.6(LINC01498):​n.206+2409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.995 in 152,342 control chromosomes in the GnomAD database, including 75,426 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 1.0 (75426 hom., cov: 32)
• Consequence: LINC01498 ENST00000502160.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01498	ENST00000502160.6	n.206+2409G>A		intron_variant	Intron 2 of 17	5

Frequencies

GnomAD3 genomes AF: 0.995 AC: 151476 AN: 152224 Hom.: 75367 Cov.: 32

Gnomad AFR AF: 0.999

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.999

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 0.991

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.998

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

GnomAD4 genome AF: 0.995 AC: 151594 AN: 152342 Hom.: 75426 Cov.: 32 AF XY: 0.995 AC XY: 74142 AN XY: 74496

African (AFR) AF: 0.999 AC: 41513 AN: 41570

American (AMR) AF: 0.999 AC: 15292 AN: 15306

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3471 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5180 AN: 5180

South Asian (SAS) AF: 0.998 AC: 4815 AN: 4826

European-Finnish (FIN) AF: 0.991 AC: 10529 AN: 10628

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67481 AN: 68042

Other (OTH) AF: 0.998 AC: 2107 AN: 2112

Alfa AF: 0.995 Hom.: 27812

Bravo AF: 0.996

Asia WGS AF: 0.999 AC: 3475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.068
DANN	Benign	0.33
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs918304; hg19: chr12-108877541;