rs17490390

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503048.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01470	ENST00000503048.1	TSL:4	n.193+85566C>T		intron	N/A

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

African (AFR) AF: 0.0876 AC: 3633 AN: 41488

American (AMR) AF: 0.0877 AC: 1338 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5162

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4816

European-Finnish (FIN) AF: 0.134 AC: 1412 AN: 10550

Middle Eastern (MID) AF: 0.107 AC: 31 AN: 290

European-Non Finnish (NFE) AF: 0.111 AC: 7535 AN: 67978

Other (OTH) AF: 0.0929 AC: 196 AN: 2110

Alfa AF: 0.101 Hom.: 471

Bravo AF: 0.0939

Asia WGS AF: 0.0160 AC: 57 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.49
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17490390; hg19: chr5-152362706;