rs3858961

chr15-80315372-G-Achr15-80315372-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033833.1(LINC00927):n.250+26184C>T variant causes a intron, non coding transcript 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 NR_033833.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00927	NR_033833.1	n.250+26184C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00927	ENST00000558913.5	n.213+26184C>T		intron_variant, non_coding_transcript_variant		1
LINC00927	ENST00000558244.2	n.250+26184C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.0809

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0857 Hom.: 1593

Bravo AF: 0.148

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3858961; hg19: chr15-80607714;