rs17113771

Variant names:

• chr5-152898460-C-T
• rs17113771
• ENST00000503048.1:n.193+170252G>A

Variant summary

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

The ENST00000503048.1(LINC01470):​n.193+170252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,996 control chromosomes in the GnomAD database, including 7,372 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 0.30 (7372 hom., cov: 32)
• Consequence: LINC01470 ENST00000503048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01470	NR_109877.1	n.178+67781G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01470	ENST00000503048.1	n.193+170252G>A		intron_variant	Intron 2 of 3	4
LINC01470	ENST00000511419.5	n.165-12832G>A		intron_variant	Intron 2 of 2	3
LINC01470	ENST00000522300.5	n.178+67781G>A		intron_variant	Intron 2 of 4	2
LINC01470	ENST00000663464.1	n.406+67781G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45958 AN: 151878 Hom.: 7356 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.303 AC: 46000 AN: 151996 Hom.: 7372 Cov.: 32 AF XY: 0.299 AC XY: 22238 AN XY: 74310

African (AFR) AF: 0.381 AC: 15794 AN: 41444

American (AMR) AF: 0.241 AC: 3684 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3466

East Asian (EAS) AF: 0.0661 AC: 342 AN: 5172

South Asian (SAS) AF: 0.319 AC: 1533 AN: 4802

European-Finnish (FIN) AF: 0.282 AC: 2985 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19744 AN: 67946

Other (OTH) AF: 0.295 AC: 624 AN: 2112

Alfa AF: 0.285 Hom.: 2942

Bravo AF: 0.300

Asia WGS AF: 0.172 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.24
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs17113771; hg19: chr5-152278020;