chr20-3471064-T-G

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.59
Variant links:
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
ATRNNM_139321.3 linkuse as main transcriptc.-44T>G 5_prime_UTR_variant 1/29 ENST00000262919.10
ATRNNM_001207047.3 linkuse as main transcriptc.-9T>G 5_prime_UTR_variant 1/25
ATRNNM_001323332.2 linkuse as main transcriptc.-44T>G 5_prime_UTR_variant 1/26
ATRNNM_139322.4 linkuse as main transcriptc.-44T>G 5_prime_UTR_variant 1/25

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATRNENST00000262919.10 linkuse as main transcriptc.-44T>G 5_prime_UTR_variant 1/295 NM_139321.3 P2O75882-1
ATRNENST00000446916.2 linkuse as main transcript upstream_gene_variant 1 A2O75882-2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
149178
Hom.:
0
Cov.:
33
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00175
AC:
2067
AN:
1179842
Hom.:
0
Cov.:
32
AF XY:
0.00162
AC XY:
943
AN XY:
583862
show subpopulations
Gnomad4 AFR exome
AF:
0.00404
Gnomad4 AMR exome
AF:
0.00240
Gnomad4 ASJ exome
AF:
0.00596
Gnomad4 EAS exome
AF:
0.00786
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.00647
Gnomad4 NFE exome
AF:
0.00138
Gnomad4 OTH exome
AF:
0.00359
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
149290
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
72982
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

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 submitterclinical testingPreventionGenetics, part of Exact SciencesJun 27, 2019This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
18
DANN
Benign
0.89

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-3451711; API