11-29456053-A-T

Variant summary

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

The ENST00000527727.1(LINC03096):n.256A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 151,304 control chromosomes in the GnomAD database, including 733 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 0.082 (733 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC03096 ENST00000527727.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

LINC03096 (HGNC:56743): (long intergenic non-protein coding RNA 3096)

LINC02755 (HGNC:54275): (long intergenic non-protein coding RNA 2755)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02755	NR_183754.1	n.209-60601T>A		intron_variant, non_coding_transcript_variant
LINC02755	NR_183753.1	n.301+64071T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03096	ENST00000527727.1	n.256A>T		non_coding_transcript_exon_variant	3/6	4
LINC02755	ENST00000657392.1	n.314+75235T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0815 AC: 12323 AN: 151190 Hom.: 724 Cov.: 30

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0532

Gnomad EAS AF: 0.000988

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0885

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0817 AC: 12355 AN: 151304 Hom.: 733 Cov.: 30 AF XY: 0.0804 AC XY: 5939 AN XY: 73898

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.0532

Gnomad4 EAS AF: 0.000990

Gnomad4 SAS AF: 0.0436

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0199 Hom.: 11

Bravo AF: 0.101

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.19
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488788; hg19: chr11-29477600;