rs17490390

Positions:

• chr5-152983146-G-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01470	ENST00000503048.1	n.193+85566C>T		intron_variant, non_coding_transcript_variant		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;