11-29456053-A-T

Variant names:

• chr11-29456053-A-T
• rs10488788
• ENST00000527727.1:n.256A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527727.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02755	NR_183753.1		n.301+64071T>A		intron	N/A
	LINC02755	NR_183754.1		n.209-60601T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03096	ENST00000527727.1	TSL:4	n.256A>T		non_coding_transcript_exon	Exon 3 of 6
	LINC02755	ENST00000525097.1	TSL:3	n.154-60601T>A		intron	N/A
	LINC02755	ENST00000528553.2	TSL:3	n.286+75235T>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.119 AC: 4909 AN: 41246

American (AMR) AF: 0.197 AC: 2983 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.0532 AC: 184 AN: 3460

East Asian (EAS) AF: 0.000990 AC: 5 AN: 5048

South Asian (SAS) AF: 0.0436 AC: 210 AN: 4814

European-Finnish (FIN) AF: 0.0254 AC: 266 AN: 10472

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0525 AC: 3564 AN: 67836

Other (OTH) AF: 0.0872 AC: 183 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.75
PhyloP100		-1.2
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10488788; hg19: chr11-29477600;