ENST00000642825.1:c.-202-17609G>A

Variant names:

• chr7-17278688-G-A
• rs13236243
• ENST00000642825.1:c.-202-17609G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642825.1(AHR):​c.-202-17609G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,032 control chromosomes in the GnomAD database, including 32,728 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 0.65 (32728 hom., cov: 32)
• Consequence: AHR ENST00000642825.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 14 publications found

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 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

ENSG00000237773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642825.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHR	ENST00000642825.1		c.-202-17609G>A		intron	N/A	ENSP00000495987.1
	ENSG00000237773	ENST00000433005.2	TSL:2	n.572+7555C>T		intron	N/A
	ENSG00000237773	ENST00000452249.7	TSL:3	n.536+7555C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98891 AN: 151914 Hom.: 32727 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.651 AC: 98916 AN: 152032 Hom.: 32728 Cov.: 32 AF XY: 0.648 AC XY: 48204 AN XY: 74334

African (AFR) AF: 0.571 AC: 23676 AN: 41456

American (AMR) AF: 0.515 AC: 7861 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2504 AN: 3466

East Asian (EAS) AF: 0.629 AC: 3245 AN: 5162

South Asian (SAS) AF: 0.613 AC: 2951 AN: 4816

European-Finnish (FIN) AF: 0.766 AC: 8097 AN: 10570

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48291 AN: 67968

Other (OTH) AF: 0.672 AC: 1423 AN: 2116

Alfa AF: 0.685 Hom.: 60334

Bravo AF: 0.630

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.32
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs13236243; hg19: chr7-17318312;