Genetic Variant AHR:c.-202-10753A>T (chr7-17285544-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000642825.1(AHR):c.-202-10753A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,062 control chromosomes in the GnomAD database, including 2,283 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 0.16 ( 2283 hom., cov: 32)

Consequence

AHR
ENST00000642825.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.588

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:

ENSG00000237773 (HGNC:):

ENSG00000237773 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101927609	XR_007060230.1 link	n.636+699T>A	intron_variant	Intron 4 of 5
LOC101927609	XR_007060231.1 link	n.494+699T>A	intron_variant	Intron 3 of 4
LOC101927609	XR_007060232.1 link	n.494+699T>A	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
AHR	ENST00000642825.1 link	c.-202-10753A>T	intron_variant	Intron 3 of 14	ENSP00000495987.1	A0A2R8Y7G1
ENSG00000237773	ENST00000670927.1 link	n.1305T>A	non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000237773	ENST00000671621.1 link	n.1132T>A	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24482

AN:

151944

Hom.:

2272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.161

AC:

24507

AN:

152062

Hom.:

2283

Cov.:

AF XY:

0.164

AC XY:

12190

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.165

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.0608

Hom.:

Bravo

AF:

0.174

Asia WGS

AF:

0.231

AC:

803

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.1

DANN

Benign

0.42

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over