rs2745061

chr20-45443556-C-T

Variant summary

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

The NR_159957.1(LOC105372631):n.351-4041C>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 0.113 in 151,786 control chromosomes in the GnomAD database, including 1,263 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 0.11 (1263 hom., cov: 32)
• Consequence: LOC105372631 NR_159957.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

Genes affected

(HGNC:):

PIGT (HGNC:14938): (phosphatidylinositol glycan anchor biosynthesis class T) This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This protein is an essential component of the multisubunit enzyme, GPI transamidase. GPI transamidase mediates GPI anchoring in the endoplasmic reticulum, by catalyzing the transfer of fully assembled GPI units to proteins. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372631	NR_159957.1	n.351-4041C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000617473.1	n.1094+3676G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17119 AN: 151700 Hom.: 1261 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.124

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.113 AC: 17119 AN: 151786 Hom.: 1263 Cov.: 32 AF XY: 0.115 AC XY: 8519 AN XY: 74112

Gnomad4 AFR AF: 0.0255

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.0807

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.123

Alfa AF: 0.134 Hom.: 427

Bravo AF: 0.113

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.8
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2745061; hg19: chr20-44072196;