chr1-26787956-G-A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_017837.4(PIGV):​c.-370G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,460 control chromosomes in the GnomAD database, including 320 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 319 hom., cov: 32)
Exomes 𝑓: 0.075 ( 1 hom. )

Consequence

PIGV
NM_017837.4 5_prime_UTR

Scores

1
1

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.98
Variant links:
Genes affected
PIGV (HGNC:26031): (phosphatidylinositol glycan anchor biosynthesis class V) This gene encodes a mannosyltransferase enzyme involved in the biosynthesis of glycosylphosphatidylinositol (GPI). GPI is a complex glycolipid that functions as a membrane anchor for many proteins and plays a role in multiple cellular processes including protein sorting and signal transduction. The encoded protein is localized to the endoplasmic reticulum and transfers the second mannose to the GPI backbone. Mutations in this gene are associated with hyperphosphatasia cognitive disability syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 1-26787956-G-A is Benign according to our data. Variant chr1-26787956-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 368873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0778 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PIGVNM_017837.4 linkuse as main transcriptc.-370G>A 5_prime_UTR_variant 1/4 ENST00000674202.1 NP_060307.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PIGVENST00000674202.1 linkuse as main transcriptc.-370G>A 5_prime_UTR_variant 1/4 NM_017837.4 ENSP00000501479 P1

Frequencies

GnomAD3 genomes
AF:
0.0565
AC:
8595
AN:
152172
Hom.:
318
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0190
Gnomad AMI
AF:
0.0592
Gnomad AMR
AF:
0.0538
Gnomad ASJ
AF:
0.0501
Gnomad EAS
AF:
0.0197
Gnomad SAS
AF:
0.0486
Gnomad FIN
AF:
0.0832
Gnomad MID
AF:
0.0446
Gnomad NFE
AF:
0.0796
Gnomad OTH
AF:
0.0540
GnomAD4 exome
AF:
0.0747
AC:
13
AN:
174
Hom.:
1
Cov.:
0
AF XY:
0.0821
AC XY:
11
AN XY:
134
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.167
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0743
Gnomad4 OTH exome
AF:
0.167
GnomAD4 genome
AF:
0.0565
AC:
8601
AN:
152286
Hom.:
319
Cov.:
32
AF XY:
0.0563
AC XY:
4190
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.0191
Gnomad4 AMR
AF:
0.0536
Gnomad4 ASJ
AF:
0.0501
Gnomad4 EAS
AF:
0.0195
Gnomad4 SAS
AF:
0.0489
Gnomad4 FIN
AF:
0.0832
Gnomad4 NFE
AF:
0.0795
Gnomad4 OTH
AF:
0.0539
Alfa
AF:
0.0642
Hom.:
48
Bravo
AF:
0.0522
Asia WGS
AF:
0.0390
AC:
136
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Hyperphosphatasia-intellectual disability syndrome Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not provided Benign:1
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.36
CADD
Benign
19
DANN
Uncertain
0.98

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs71636780; hg19: chr1-27114447; API