rs713150

Positions:

• chr7-17300533-G-C
• chr7-17300533-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000242057.9(AHR):​c.65+1204G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,102 control chromosomes in the GnomAD database, including 46,931 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 0.78 (46931 hom., cov: 32)
• Consequence: AHR ENST00000242057.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHR	NM_001621.5	c.65+1204G>C		intron_variant		ENST00000242057.9	NP_001612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHR	ENST00000242057.9	c.65+1204G>C		intron_variant		1	NM_001621.5	ENSP00000242057	P2
AHR	ENST00000463496.1	c.65+1204G>C		intron_variant, NMD_transcript_variant		1		ENSP00000436466
AHR	ENST00000642825.1	c.20+3909G>C		intron_variant				ENSP00000495987	A2

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119044 AN: 151986 Hom.: 46896 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.783 AC: 119133 AN: 152102 Hom.: 46931 Cov.: 32 AF XY: 0.782 AC XY: 58180 AN XY: 74358

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.772

Alfa AF: 0.777 Hom.: 5384

Bravo AF: 0.781

Asia WGS AF: 0.716 AC: 2485 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs713150; hg19: chr7-17340157;