13-90061691-C-T

Variant names:

• chr13-90061691-C-T
• rs17722514
• ENST00000569476.2:n.3502-1079G>A

Variant summary

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

The ENST00000569476.2(LINC00559):​n.3502-1079G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 151,272 control chromosomes in the GnomAD database, including 328 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 0.053 (328 hom., cov: 32)
• Consequence: LINC00559 ENST00000569476.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 2 publications found

Genes affected

LINC00559 (HGNC:43703): (long intergenic non-protein coding RNA 559)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00559	NR_047489.1	n.3500-1079G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00559	ENST00000569476.2	n.3502-1079G>A		intron_variant	Intron 5 of 5	1
LINC00559	ENST00000647679.1	n.1635-1082G>A		intron_variant	Intron 6 of 6
LINC00559	ENST00000653351.1	n.650-1079G>A		intron_variant	Intron 4 of 4
LINC00559	ENST00000654320.1	n.1081-1079G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 7944 AN: 151154 Hom.: 329 Cov.: 32

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00368

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0525 AC: 7942 AN: 151272 Hom.: 328 Cov.: 32 AF XY: 0.0521 AC XY: 3849 AN XY: 73866

African (AFR) AF: 0.0131 AC: 543 AN: 41346

American (AMR) AF: 0.0643 AC: 972 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3456

East Asian (EAS) AF: 0.00369 AC: 19 AN: 5150

South Asian (SAS) AF: 0.112 AC: 540 AN: 4806

European-Finnish (FIN) AF: 0.0236 AC: 247 AN: 10478

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0746 AC: 5046 AN: 67606

Other (OTH) AF: 0.0586 AC: 123 AN: 2100

Alfa AF: 0.0406 Hom.: 34

Bravo AF: 0.0508

Asia WGS AF: 0.0490 AC: 169 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.64
PhyloP100		-0.20
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: rs17722514; hg19: chr13-90713945;