Variant 5-413406-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001377236.1(AHRR):c.414G>A(p.Thr138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,613,802 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00090 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0014 ( 3 hom. )

Consequence

AHRR
NM_001377236.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.42

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]

AHRR links:

PDCD6-AHRR (HGNC:):

PDCD6-AHRR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 5-413406-G-A is Benign according to our data. Variant chr5-413406-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2655243.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.42 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
AHRR	NM_001377236.1 linkuse as main transcript	c.414G>A	p.Thr138=	synonymous_variant	5/11	ENST00000684583.1
PDCD6-AHRR	NR_165159.2 linkuse as main transcript	n.707G>A		non_coding_transcript_exon_variant	7/14
AHRR	NM_001377239.1 linkuse as main transcript	c.414G>A	p.Thr138=	synonymous_variant	5/11
PDCD6-AHRR	NR_165163.2 linkuse as main transcript	n.707G>A		non_coding_transcript_exon_variant	7/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
AHRR	ENST00000684583.1 linkuse as main transcript	c.414G>A	p.Thr138=	synonymous_variant	5/11		NM_001377236.1	P1
AHRR	ENST00000316418.10 linkuse as main transcript	c.414G>A	p.Thr138=	synonymous_variant	5/11	1		P1
AHRR	ENST00000510400.5 linkuse as main transcript	c.414G>A	p.Thr138=	synonymous_variant	5/6	4
AHRR	ENST00000514523.1 linkuse as main transcript	c.-37G>A		5_prime_UTR_variant	5/6	4

Frequencies

GnomAD3 genomes

AF:

0.000901

AC:

137

AN:

152058

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000197

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00123

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00166

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000910

AC:

227

AN:

249406

Hom.:

AF XY:

0.000968

AC XY:

131

AN XY:

135318

show subpopulations

Gnomad AFR exome

AF:

0.0000646

Gnomad AMR exome

AF:

0.000174

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000589

Gnomad FIN exome

AF:

0.00209

Gnomad NFE exome

AF:

0.00138

Gnomad OTH exome

AF:

0.000165

GnomAD4 exome

AF:

0.00138

AC:

2013

AN:

1461626

Hom.:

Cov.:

AF XY:

0.00135

AC XY:

978

AN XY:

727118

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.000224

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000557

Gnomad4 FIN exome

AF:

0.00183

Gnomad4 NFE exome

AF:

0.00162

Gnomad4 OTH exome

AF:

0.000795

GnomAD4 genome

AF:

0.000900

AC:

137

AN:

152176

Hom.:

Cov.:

AF XY:

0.000927

AC XY:

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.000120

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00123

Gnomad4 NFE

AF:

0.00166

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000869

Hom.:

Bravo

AF:

0.000801

EpiCase

AF:

0.00115

EpiControl

AF:

0.00124

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2022

AHRR: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

1.6

DANN

Benign

0.80

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over