chr20-3471064-T-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_139321.3(ATRN):c.-44T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ATRN
NM_139321.3 5_prime_UTR
NM_139321.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.59
Genes affected
ATRN (HGNC:885): (attractin) This gene encodes both membrane-bound and secreted protein isoforms. A membrane-bound isoform exhibits sequence similarity with the mouse mahogany protein, a receptor involved in controlling obesity. A secreted isoform is involved in the initial immune cell clustering during inflammatory responses that may regulate the chemotactic activity of chemokines. [provided by RefSeq, Apr 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 20-3471064-T-G is Benign according to our data. Variant chr20-3471064-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 3041871.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRN | NM_139321.3 | c.-44T>G | 5_prime_UTR_variant | 1/29 | ENST00000262919.10 | ||
ATRN | NM_001207047.3 | c.-9T>G | 5_prime_UTR_variant | 1/25 | |||
ATRN | NM_001323332.2 | c.-44T>G | 5_prime_UTR_variant | 1/26 | |||
ATRN | NM_139322.4 | c.-44T>G | 5_prime_UTR_variant | 1/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRN | ENST00000262919.10 | c.-44T>G | 5_prime_UTR_variant | 1/29 | 5 | NM_139321.3 | P2 | ||
ATRN | ENST00000446916.2 | upstream_gene_variant | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 149178Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 genomes
AF:
AC:
0
AN:
149178
Hom.:
Cov.:
33
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00175 AC: 2067AN: 1179842Hom.: 0 Cov.: 32 AF XY: 0.00162 AC XY: 943AN XY: 583862
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2067
AN:
1179842
Hom.:
Cov.:
32
AF XY:
AC XY:
943
AN XY:
583862
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 149290Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 72982
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
149290
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
72982
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ATRN-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 27, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.