5-153125369-A-G

Variant names:

• chr5-153125369-A-G
• rs1438949
• ENST00000503048.1:n.92-56556T>C

Variant summary

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

The ENST00000503048.1(LINC01470):​n.92-56556T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,162 control chromosomes in the GnomAD database, including 65,583 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 0.93 (65583 hom., cov: 30)
• Consequence: LINC01470 ENST00000503048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.934 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.92-56556T>C		intron_variant	Intron 1 of 3	4
ENSG00000306270	ENST00000816601.1	n.116+12425T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141114 AN: 152044 Hom.: 65529 Cov.: 30

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.928 AC: 141225 AN: 152162 Hom.: 65583 Cov.: 30 AF XY: 0.930 AC XY: 69169 AN XY: 74366

African (AFR) AF: 0.895 AC: 37133 AN: 41500

American (AMR) AF: 0.937 AC: 14320 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3244 AN: 3472

East Asian (EAS) AF: 0.939 AC: 4829 AN: 5144

South Asian (SAS) AF: 0.947 AC: 4556 AN: 4812

European-Finnish (FIN) AF: 0.952 AC: 10104 AN: 10608

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63920 AN: 68018

Other (OTH) AF: 0.919 AC: 1944 AN: 2116

Alfa AF: 0.935 Hom.: 191079

Bravo AF: 0.925

Asia WGS AF: 0.914 AC: 3179 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs1438949; hg19: chr5-152504929;