rs13236243

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-17278688-G-A
• chr7-17278688-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927609	XR_007060234.1	n.845+2553C>T		intron_variant	Intron 5 of 11
LOC101927609	XR_007060235.1	n.709+2553C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHR	ENST00000642825.1	c.-202-17609G>A		intron_variant	Intron 3 of 14			ENSP00000495987.1
ENSG00000237773	ENST00000433005.2	n.572+7555C>T		intron_variant	Intron 2 of 5	2
ENSG00000237773	ENST00000452249.7	n.536+7555C>T		intron_variant	Intron 3 of 4	3

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 v4.3

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;