5-152908893-T-G

Variant names:

• chr5-152908893-T-G
• rs4262150
• ENST00000503048.1:n.193+159819A>C

Variant summary

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

The ENST00000522300.5(LINC01470):​n.178+57348A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 151,830 control chromosomes in the GnomAD database, including 32,052 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 0.64 (32052 hom., cov: 29)
• Consequence: LINC01470 ENST00000522300.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522300.5. 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
	LINC01470	NR_109877.1		n.178+57348A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01470	ENST00000503048.1	TSL:4	n.193+159819A>C		intron	N/A
	LINC01470	ENST00000511419.5	TSL:3	n.165-23265A>C		intron	N/A
	LINC01470	ENST00000522300.5	TSL:2	n.178+57348A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97330 AN: 151710 Hom.: 32028 Cov.: 29

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.642 AC: 97400 AN: 151830 Hom.: 32052 Cov.: 29 AF XY: 0.645 AC XY: 47833 AN XY: 74152

African (AFR) AF: 0.495 AC: 20473 AN: 41400

American (AMR) AF: 0.723 AC: 11035 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2320 AN: 3470

East Asian (EAS) AF: 0.933 AC: 4772 AN: 5116

South Asian (SAS) AF: 0.671 AC: 3217 AN: 4794

European-Finnish (FIN) AF: 0.669 AC: 7056 AN: 10546

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46358 AN: 67934

Other (OTH) AF: 0.654 AC: 1377 AN: 2106

Alfa AF: 0.654 Hom.: 36997

Bravo AF: 0.642

Asia WGS AF: 0.812 AC: 2822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs4262150; hg19: chr5-152288453;