Genetic Variant ENST00000659284.2:n.13G>A (chr7-17298523-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000659284.2(ENSG00000237773):n.13G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 316,128 control chromosomes in the GnomAD database, including 7,455 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.23 ( 4389 hom., cov: 21)

Exomes 𝑓: 0.16 ( 3066 hom. )

Consequence

ENSG00000237773
ENST00000659284.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Publications

25 publications found

Variant links:

Genes affected

ENSG00000237773 (HGNC:):

ENSG00000237773 links:

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 Gene-Disease associations (from GenCC):

retinitis pigmentosa 85
Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
retinitis pigmentosa
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
foveal hypoplasia
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

AHR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHR	NM_001621.5 link	c.-742C>T		upstream_gene_variant		ENST00000242057.9	NP_001612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHR	ENST00000242057.9 link	c.-742C>T		upstream_gene_variant		1	NM_001621.5	ENSP00000242057.4

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

30732

AN:

133798

Hom.:

4366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.145

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.204

GnomAD4 exome

AF:

0.162

AC:

29575

AN:

182264

Hom.:

3066

Cov.:

AF XY:

0.160

AC XY:

14859

AN XY:

92628

show subpopulations

African (AFR)

AF:

0.387

AC:

2016

AN:

5214

American (AMR)

AF:

0.331

AC:

1730

AN:

5230

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

843

AN:

7146

East Asian (EAS)

AF:

0.319

AC:

5330

AN:

16720

South Asian (SAS)

AF:

0.203

AC:

331

AN:

1632

European-Finnish (FIN)

AF:

0.116

AC:

1793

AN:

15402

Middle Eastern (MID)

AF:

0.133

AC:

128

AN:

964

European-Non Finnish (NFE)

AF:

0.129

AC:

15218

AN:

117768

Other (OTH)

AF:

0.179

AC:

2186

AN:

12188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1083

2166

3250

4333

5416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

224

336

448

560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.230

AC:

30805

AN:

133864

Hom.:

4389

Cov.:

AF XY:

0.235

AC XY:

14993

AN XY:

63902

show subpopulations

African (AFR)

AF:

0.398

AC:

14033

AN:

35288

American (AMR)

AF:

0.321

AC:

4096

AN:

12750

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

423

AN:

3306

East Asian (EAS)

AF:

0.276

AC:

1198

AN:

4348

South Asian (SAS)

AF:

0.214

AC:

868

AN:

4058

European-Finnish (FIN)

AF:

0.146

AC:

1094

AN:

7510

Middle Eastern (MID)

AF:

0.137

AC:

AN:

234

European-Non Finnish (NFE)

AF:

0.135

AC:

8599

AN:

63690

Other (OTH)

AF:

0.203

AC:

373

AN:

1834

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

997

1993

2990

3986

4983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.139

Hom.:

1061

Bravo

AF:

0.241

Asia WGS

AF:

0.230

AC:

800

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

2.6

(source)

DANN

Benign

0.95

PhyloP100

-1.6

PromoterAI

-0.24

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over