5-153124378-C-T

Variant names:

• chr5-153124378-C-T
• rs57917647
• ENST00000503048.1:n.92-55565G>A

Variant summary

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

The ENST00000503048.1(LINC01470):​n.92-55565G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0386 in 151,854 control chromosomes in the GnomAD database, including 207 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 0.039 (207 hom., cov: 30)
• Consequence: LINC01470 ENST00000503048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

Genes affected

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

ENSG00000306270 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0807 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01470	ENST00000503048.1	TSL:4	n.92-55565G>A		intron	N/A
	ENSG00000306270	ENST00000816601.1		n.116+13416G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5855 AN: 151738 Hom.: 205 Cov.: 30

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00769

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0386 AC: 5869 AN: 151854 Hom.: 207 Cov.: 30 AF XY: 0.0396 AC XY: 2933 AN XY: 74152

African (AFR) AF: 0.0830 AC: 3438 AN: 41402

American (AMR) AF: 0.0199 AC: 303 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5162

South Asian (SAS) AF: 0.00770 AC: 37 AN: 4808

European-Finnish (FIN) AF: 0.0784 AC: 824 AN: 10506

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0167 AC: 1133 AN: 67954

Other (OTH) AF: 0.0289 AC: 61 AN: 2110

Alfa AF: 0.0169 Hom.: 5

Bravo AF: 0.0368

Asia WGS AF: 0.00867 AC: 30 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.68
PhyloP100		-1.0
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: rs57917647; hg19: chr5-152503938;