Genetic Variant AHR:p.Asn44Asn (chr7-17310002-T-C) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001621.5(AHR):c.132T>C(p.Asn44Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 1,613,268 control chromosomes in the GnomAD database, including 5,833 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.068 ( 447 hom., cov: 32)

Exomes 𝑓: 0.082 ( 5386 hom. )

Consequence

AHR
NM_001621.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.669

Variant links:

Genes affected

AHR (HGNC:348): (aryl hydrocarbon receptor) The protein encoded by this gene is a ligand-activated helix-loop-helix transcription factor involved in the regulation of biological responses to planar aromatic hydrocarbons. This receptor has been shown to regulate xenobiotic-metabolizing enzymes such as cytochrome P450. Before ligand binding, the encoded protein is sequestered in the cytoplasm; upon ligand binding, this protein moves to the nucleus and stimulates transcription of target genes. [provided by RefSeq, Sep 2015]

AHR links:

ENSG00000283321 (HGNC:):

ENSG00000283321 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 7-17310002-T-C is Benign according to our data. Variant chr7-17310002-T-C is described in ClinVar as [Benign]. Clinvar id is 1166758.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.669 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHR	NM_001621.5 link	c.132T>C	p.Asn44Asn	synonymous_variant	Exon 2 of 11	ENST00000242057.9	NP_001612.1	P35869A0A024R9Z8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
AHR	ENST00000242057.9 link	c.132T>C	p.Asn44Asn	synonymous_variant	Exon 2 of 11	1	NM_001621.5	ENSP00000242057.4	P35869
ENSG00000283321	ENST00000637807.1 link	c.102T>C	p.Asn34Asn	synonymous_variant	Exon 2 of 12	5		ENSP00000490530.1	A0A1B0GVI7
AHR	ENST00000463496.1 link	n.132T>C		non_coding_transcript_exon_variant	Exon 2 of 12	1		ENSP00000436466.1	P35869
AHR	ENST00000642825.1 link	c.87T>C	p.Asn29Asn	synonymous_variant	Exon 6 of 15			ENSP00000495987.1	A0A2R8Y7G1

Frequencies

GnomAD3 genomes

AF:

0.0681

AC:

10357

AN:

152126

Hom.:

447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0293

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.0392

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.0335

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0874

Gnomad OTH

AF:

0.0569

GnomAD3 exomes

AF:

0.0771

AC:

19364

AN:

251286

Hom.:

891

AF XY:

0.0810

AC XY:

10996

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.0289

Gnomad AMR exome

AF:

0.0311

Gnomad ASJ exome

AF:

0.0373

Gnomad EAS exome

AF:

0.0357

Gnomad SAS exome

AF:

0.109

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.0870

Gnomad OTH exome

AF:

0.0747

GnomAD4 exome

AF:

0.0817

AC:

119372

AN:

1461024

Hom.:

5386

Cov.:

AF XY:

0.0832

AC XY:

60453

AN XY:

726796

show subpopulations

Gnomad4 AFR exome

AF:

0.0289

Gnomad4 AMR exome

AF:

0.0333

Gnomad4 ASJ exome

AF:

0.0408

Gnomad4 EAS exome

AF:

0.0337

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.144

Gnomad4 NFE exome

AF:

0.0836

Gnomad4 OTH exome

AF:

0.0728

GnomAD4 genome

AF:

0.0680

AC:

10347

AN:

152244

Hom.:

447

Cov.:

AF XY:

0.0706

AC XY:

5253

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0292

Gnomad4 AMR

AF:

0.0392

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.0332

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.143

Gnomad4 NFE

AF:

0.0873

Gnomad4 OTH

AF:

0.0568

Alfa

AF:

0.0796

Hom.:

1213

Bravo

AF:

0.0563

Asia WGS

AF:

0.0790

AC:

272

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

AHR-related disorder

Benign:1

Jul 11, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as 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

-0.57

CADD

Benign

7.4

DANN

Benign

0.63

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