ENST00000503048.1:n.193+85566C>T

Variant names:

• chr5-152983146-G-A
• rs17490390
• ENST00000503048.1:n.193+85566C>T

Variant summary

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

The ENST00000503048.1(LINC01470):​n.193+85566C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0968 in 152,034 control chromosomes in the GnomAD database, including 781 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 0.097 (781 hom., cov: 32)
• Consequence: LINC01470 ENST00000503048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

Genes affected

LINC01470 (HGNC:51105): (long intergenic non-protein coding RNA 1470)

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 = 0.109 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
LINC01470	ENST00000503048.1	n.193+85566C>T		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14718 AN: 151916 Hom.: 781 Cov.: 32

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0968 AC: 14716 AN: 152034 Hom.: 781 Cov.: 32 AF XY: 0.0951 AC XY: 7068 AN XY: 74284

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.0877

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0929

Alfa AF: 0.101 Hom.: 197

Bravo AF: 0.0939

Asia WGS AF: 0.0160 AC: 57 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17490390; hg19: chr5-152362706;