rs17312725

Variant names:

• chr15-80313569-A-G
• rs17312725
• ENST00000558913.5:n.214-25716T>C

Variant summary

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

The ENST00000558913.5(LINC00927):​n.214-25716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,262 control chromosomes in the GnomAD database, including 1,639 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 0.14 (1639 hom., cov: 33)
• Consequence: LINC00927 ENST00000558913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 3 publications found

Genes affected

LINC00927 (HGNC:27522): (long intergenic non-protein coding RNA 927)

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 (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00927	NR_033833.1	n.251-25716T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00927	ENST00000558913.5	n.214-25716T>C		intron_variant	Intron 1 of 2	1
LINC00927	ENST00000558244.2	n.251-25716T>C		intron_variant	Intron 1 of 2	3
LINC00927	ENST00000794379.1	n.223-25716T>C		intron_variant	Intron 1 of 2
LINC00927	ENST00000794380.1	n.235-525T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20968 AN: 152142 Hom.: 1638 Cov.: 33

Gnomad AFR AF: 0.0732

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.138 AC: 20983 AN: 152262 Hom.: 1639 Cov.: 33 AF XY: 0.138 AC XY: 10244 AN XY: 74438

African (AFR) AF: 0.0735 AC: 3052 AN: 41550

American (AMR) AF: 0.174 AC: 2657 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 616 AN: 3472

East Asian (EAS) AF: 0.0123 AC: 64 AN: 5184

South Asian (SAS) AF: 0.201 AC: 968 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1670 AN: 10606

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11400 AN: 68016

Other (OTH) AF: 0.156 AC: 330 AN: 2112

Alfa AF: 0.156 Hom.: 5072

Bravo AF: 0.135

Asia WGS AF: 0.0990 AC: 345 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	1.0
DANN	Benign	0.42
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs17312725; hg19: chr15-80605911;