5-153160794-C-T

Variant names:

• chr5-153160794-C-T
• rs2910032
• ENST00000503048.1:n.91+62659G>A

Variant summary

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

The ENST00000503048.1(LINC01470):​n.91+62659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,746 control chromosomes in the GnomAD database, including 21,453 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 0.52 (21453 hom., cov: 31)
• Consequence: LINC01470 ENST00000503048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 17 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 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.91+62659G>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79360 AN: 151628 Hom.: 21431 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.523 AC: 79422 AN: 151746 Hom.: 21453 Cov.: 31 AF XY: 0.530 AC XY: 39329 AN XY: 74136

African (AFR) AF: 0.422 AC: 17431 AN: 41312

American (AMR) AF: 0.621 AC: 9458 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1854 AN: 3470

East Asian (EAS) AF: 0.825 AC: 4255 AN: 5160

South Asian (SAS) AF: 0.670 AC: 3224 AN: 4814

European-Finnish (FIN) AF: 0.570 AC: 5996 AN: 10520

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35394 AN: 67920

Other (OTH) AF: 0.511 AC: 1081 AN: 2114

Alfa AF: 0.528 Hom.: 33975

Bravo AF: 0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2910032; hg19: chr5-152540354;