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GeneBe

5-353823-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001377236.1(AHRR):c.156G>A(p.Pro52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00237 in 1,614,052 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0024 ( 7 hom. )

Consequence

AHRR
NM_001377236.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.15
Variant links:
Genes affected
AHRR (HGNC:346): (aryl hydrocarbon receptor repressor) The protein encoded by this gene participates in the aryl hydrocarbon receptor (AhR) signaling cascade, which mediates dioxin toxicity, and is involved in regulation of cell growth and differentiation. It functions as a feedback modulator by repressing AhR-dependent gene expression. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jun 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-353823-G-A is Benign according to our data. Variant chr5-353823-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 726872.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-4.15 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AHRRNM_001377236.1 linkuse as main transcriptc.156G>A p.Pro52= synonymous_variant 3/11 ENST00000684583.1
PDCD6-AHRRNR_165159.2 linkuse as main transcriptn.449G>A non_coding_transcript_exon_variant 5/14
AHRRNM_001377239.1 linkuse as main transcriptc.156G>A p.Pro52= synonymous_variant 3/11
PDCD6-AHRRNR_165163.2 linkuse as main transcriptn.449G>A non_coding_transcript_exon_variant 5/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AHRRENST00000684583.1 linkuse as main transcriptc.156G>A p.Pro52= synonymous_variant 3/11 NM_001377236.1 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00166
AC:
252
AN:
152192
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000772
Gnomad AMI
AF:
0.0263
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00271
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00139
AC:
346
AN:
249316
Hom.:
0
AF XY:
0.00146
AC XY:
198
AN XY:
135316
show subpopulations
Gnomad AFR exome
AF:
0.000646
Gnomad AMR exome
AF:
0.000203
Gnomad ASJ exome
AF:
0.000796
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.0000929
Gnomad NFE exome
AF:
0.00274
Gnomad OTH exome
AF:
0.00132
GnomAD4 exome
AF:
0.00245
AC:
3575
AN:
1461742
Hom.:
7
Cov.:
31
AF XY:
0.00235
AC XY:
1706
AN XY:
727176
show subpopulations
Gnomad4 AFR exome
AF:
0.000358
Gnomad4 AMR exome
AF:
0.000224
Gnomad4 ASJ exome
AF:
0.000612
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.0000750
Gnomad4 NFE exome
AF:
0.00311
Gnomad4 OTH exome
AF:
0.00119
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00165
AC:
252
AN:
152310
Hom.:
0
Cov.:
33
AF XY:
0.00137
AC XY:
102
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.000770
Gnomad4 AMR
AF:
0.000392
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.00271
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00215
Hom.:
0
Bravo
AF:
0.00165
EpiCase
AF:
0.00327
EpiControl
AF:
0.00302

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeMar 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
1.7
Dann
Benign
0.87

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

LitVar

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

Other links and lift over

dbSNP: rs150312721; hg19: chr5-353938; COSMIC: COSV100327113; API