ENST00000558913.5:n.213+26184C>T

Variant names:

• chr15-80315372-G-A
• rs3858961
• ENST00000558913.5:n.213+26184C>T

Variant summary

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

The ENST00000558913.5(LINC00927):​n.213+26184C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,056 control chromosomes in the GnomAD database, including 2,076 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 (2076 hom., cov: 32)
• Consequence: LINC00927 ENST00000558913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558913.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00927	NR_033833.1		n.250+26184C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00927	ENST00000558913.5	TSL:1	n.213+26184C>T		intron	N/A
	LINC00927	ENST00000558244.2	TSL:3	n.250+26184C>T		intron	N/A
	LINC00927	ENST00000794379.1		n.222+26184C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20515 AN: 151936 Hom.: 2071 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.135 AC: 20553 AN: 152056 Hom.: 2076 Cov.: 32 AF XY: 0.137 AC XY: 10207 AN XY: 74322

African (AFR) AF: 0.217 AC: 8974 AN: 41430

American (AMR) AF: 0.166 AC: 2535 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3470

East Asian (EAS) AF: 0.470 AC: 2419 AN: 5148

South Asian (SAS) AF: 0.0500 AC: 240 AN: 4800

European-Finnish (FIN) AF: 0.0809 AC: 857 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0705 AC: 4792 AN: 68002

Other (OTH) AF: 0.134 AC: 282 AN: 2112

Alfa AF: 0.0938 Hom.: 4257

Bravo AF: 0.148

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.85
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs3858961; hg19: chr15-80607714;