rs2273553

Positions:

• chr11-33076331-G-A

Variant summary

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

The NR_015451.1(LINC00294):​n.182G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.144 in 1,438,182 control chromosomes in the GnomAD database, including 16,294 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 0.13 (1573 hom., cov: 32)
  • Exomes 𝑓: 0.14 (14721 hom.)
• Consequence: LINC00294 NR_015451.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.60

Genes affected

PIGCP1 (HGNC:8961): (phosphatidylinositol glycan anchor biosynthesis class C pseudogene 1)

LINC00294 (HGNC:27456): (long intergenic non-protein coding RNA 294)

TCP11L1 (HGNC:25655): (t-complex 11 like 1) Predicted to be involved in signal transduction. Located in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00294	NR_015451.1	n.182G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGCP1	ENST00000527583.1	n.130C>T		non_coding_transcript_exon_variant	1/1
LINC00294	ENST00000631190.1	n.183G>A		non_coding_transcript_exon_variant	1/1
TCP11L1	ENST00000528962.1	c.353+3678G>A		intron_variant		3
TCP11L1	ENST00000527661.5	c.1507+3678G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20321 AN: 152046 Hom.: 1576 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.145 AC: 186329 AN: 1286018 Hom.: 14721 Cov.: 21 AF XY: 0.146 AC XY: 94459 AN XY: 648026

Gnomad4 AFR exome AF: 0.0473

Gnomad4 AMR exome AF: 0.117

Gnomad4 ASJ exome AF: 0.217

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.112

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.152

GnomAD4 genome AF: 0.133 AC: 20311 AN: 152164 Hom.: 1573 Cov.: 32 AF XY: 0.132 AC XY: 9826 AN XY: 74376

Gnomad4 AFR AF: 0.0582

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.154

Alfa AF: 0.125 Hom.: 229

Bravo AF: 0.131

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2273553; hg19: chr11-33097877;