rs2273553

Variant names:

• chr11-33076331-G-A
• rs2273553
• ENST00000527583.1:n.130C>T

Variant summary

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

The ENST00000527583.1(PIGCP1):​n.130C>T 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: PIGCP1 ENST00000527583.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.60
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00294	NR_015451.1	n.182G>A		non_coding_transcript_exon_variant	Exon 1 of 1
PIGCP1		n.33076331G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGCP1	ENST00000527583.1	n.130C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC00294	ENST00000631190.1	n.183G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
TCP11L1	ENST00000528962.1	c.352+3678G>A		intron_variant	Intron 2 of 2	3		ENSP00000436471.1
TCP11L1	ENST00000527661.5	n.1507+3678G>A		intron_variant	Intron 10 of 12	5		ENSP00000435667.1

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

African (AFR) AF: 0.0473 AC: 1457 AN: 30798

American (AMR) AF: 0.117 AC: 5192 AN: 44230

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 5358 AN: 24744

East Asian (EAS) AF: 0.111 AC: 4316 AN: 38832

South Asian (SAS) AF: 0.112 AC: 9298 AN: 83080

European-Finnish (FIN) AF: 0.167 AC: 8715 AN: 52126

Middle Eastern (MID) AF: 0.195 AC: 1059 AN: 5428

European-Non Finnish (NFE) AF: 0.150 AC: 142696 AN: 952608

Other (OTH) AF: 0.152 AC: 8238 AN: 54172

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

African (AFR) AF: 0.0582 AC: 2419 AN: 41532

American (AMR) AF: 0.138 AC: 2103 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3468

East Asian (EAS) AF: 0.118 AC: 610 AN: 5168

South Asian (SAS) AF: 0.100 AC: 483 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1740 AN: 10578

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11614 AN: 67990

Other (OTH) AF: 0.154 AC: 324 AN: 2110

Alfa AF: 0.123 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
PhyloP100		3.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2273553; hg19: chr11-33097877;