Genetic Variant PIGC:n.986C>A (chr1-172393809-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000484368.1(PIGC):n.986C>A 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 0.704 in 152,462 control chromosomes in the GnomAD database, including 40,778 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 0.70 ( 40649 hom., cov: 32)

Exomes 𝑓: 0.78 ( 129 hom. )

Consequence

PIGC
ENST00000484368.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

3 publications found

Variant links:

Genes affected

PIGC (HGNC:8960): (phosphatidylinositol glycan anchor biosynthesis class C) This gene encodes an endoplasmic reticulum associated protein that is involved in glycosylphosphatidylinositol (GPI) lipid anchor biosynthesis. The GPI lipid anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. The encoded protein is one subunit of the GPI N-acetylglucosaminyl (GlcNAc) transferase that transfers GlcNAc to phosphatidylinositol (PI) on the cytoplasmic side of the endoplasmic reticulum. Two alternatively spliced transcripts that encode the same protein have been found for this gene. A pseudogene on chromosome 11 has also been characterized. [provided by RefSeq, Jul 2008]

PIGC links:

DNM3 (HGNC:29125): (dynamin 3) This gene encodes a member of a family of guanosine triphosphate (GTP)-binding proteins that associate with microtubules and are involved in vesicular transport. The encoded protein functions in the development of megakaryocytes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

DNM3 links:

LOC102724528 (HGNC:):

LOC102724528 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNM3	NM_015569.5 link	c.2522+5000G>T		intron_variant	Intron 20 of 20	ENST00000627582.3	NP_056384.2	Q9UQ16-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNM3	ENST00000627582.3 link	c.2522+5000G>T		intron_variant	Intron 20 of 20	1	NM_015569.5	ENSP00000486701.1		Q9UQ16-3

Frequencies

GnomAD3 genomes

AF:

0.703

AC:

106861

AN:

151904

Hom.:

40618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.804

Gnomad AMR

AF:

0.808

Gnomad ASJ

AF:

0.791

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.783

Gnomad FIN

AF:

0.802

Gnomad MID

AF:

0.772

Gnomad NFE

AF:

0.831

Gnomad OTH

AF:

0.740

GnomAD4 exome

AF:

0.775

AC:

341

AN:

440

Hom.:

129

Cov.:

AF XY:

0.771

AC XY:

202

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.772

AC:

329

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.875

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.703

AC:

106931

AN:

152022

Hom.:

40649

Cov.:

AF XY:

0.707

AC XY:

52516

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.387

AC:

16020

AN:

41408

American (AMR)

AF:

0.809

AC:

12367

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.791

AC:

2744

AN:

3470

East Asian (EAS)

AF:

0.875

AC:

4531

AN:

5176

South Asian (SAS)

AF:

0.784

AC:

3781

AN:

4820

European-Finnish (FIN)

AF:

0.802

AC:

8462

AN:

10556

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.831

AC:

56500

AN:

67980

Other (OTH)

AF:

0.742

AC:

1569

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1324

2648

3971

5295

6619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.776

Hom.:

60357

Bravo

AF:

0.691

Asia WGS

AF:

0.811

AC:

2820

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.6

(source)

DANN

Benign

0.29

PhyloP100

0.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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chr1-172393809-G-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over