GeneBe

20-21705766-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001257096.2(PAX1):​c.54G>A​(p.Gly18Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PAX1
NM_001257096.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.102
Variant links:
Genes affected
PAX1 (HGNC:8615): (paired box 1) This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. This gene plays a role in pattern formation during embryogenesis and may be essential for development of the vertebral column. This gene is silenced by methylation in ovarian and cervical cancers and may be a tumor suppressor gene. Mutations in this gene are also associated with vertebral malformations. [provided by RefSeq, Mar 2012]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 20-21705766-G-A is Benign according to our data. Variant chr20-21705766-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 793592.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.102 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PAX1NM_001257096.2 linkc.54G>A p.Gly18Gly synonymous_variant Exon 1 of 5 ENST00000613128.5 NP_001244025.1 A0A087WXV5
PAX1NM_006192.5 linkc.54G>A p.Gly18Gly synonymous_variant Exon 1 of 5 NP_006183.2 P15863-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PAX1ENST00000613128.5 linkc.54G>A p.Gly18Gly synonymous_variant Exon 1 of 5 1 NM_001257096.2 ENSP00000481334.1 A0A087WXV5
PAX1ENST00000398485.6 linkc.54G>A p.Gly18Gly synonymous_variant Exon 1 of 5 5 ENSP00000381499.2 P15863-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1112198
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
530446
African (AFR)
AF:
0.00
AC:
0
AN:
22926
American (AMR)
AF:
0.00
AC:
0
AN:
8388
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14254
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26808
South Asian (SAS)
AF:
0.00
AC:
0
AN:
20668
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35422
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3170
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
936130
Other (OTH)
AF:
0.00
AC:
0
AN:
44432
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Oct 24, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
5.1
DANN
Benign
0.93
PhyloP100
0.10
PromoterAI
0.12
Neutral

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

Other links and lift over

dbSNP: rs1328189699; hg19: chr20-21686404; API