rs17137566

chr7-17320897-T-Cchr7-17320897-T-G

Variant summary

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

The NM_001621.5(AHR):c.254-1604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,072 control chromosomes in the GnomAD database, including 2,523 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 0.18 (2523 hom., cov: 32)
• Consequence: AHR NM_001621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHR	NM_001621.5	c.254-1604T>C		intron_variant		ENST00000242057.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHR	ENST00000242057.9	c.254-1604T>C		intron_variant		1	NM_001621.5	P2
AHR	ENST00000463496.1	c.254-1604T>C		intron_variant, NMD_transcript_variant		1
AHR	ENST00000642825.1	c.209-1604T>C		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26831 AN: 151952 Hom.: 2524 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.176 AC: 26840 AN: 152072 Hom.: 2523 Cov.: 32 AF XY: 0.178 AC XY: 13211 AN XY: 74338

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.183

Alfa AF: 0.168 Hom.: 3812

Bravo AF: 0.179

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.93
Dann	Benign	0.63

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: rs17137566; hg19: chr7-17360521;