chr7-17308274-T-C

Position:

• chr7-17308274-T-C

Variant summary

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

The NM_001621.5(AHR):​c.66-1662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,866 control chromosomes in the GnomAD database, including 28,273 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 0.60 (28273 hom., cov: 31)
• Consequence: AHR NM_001621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

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]

ENSG00000283321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHR	NM_001621.5	c.66-1662T>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.66-1662T>C		intron_variant		1	NM_001621.5	ENSP00000242057.4
ENSG00000283321	ENST00000637807.1	c.36-1662T>C		intron_variant		5		ENSP00000490530.1
AHR	ENST00000463496.1	n.66-1662T>C		intron_variant		1		ENSP00000436466.1
AHR	ENST00000642825.1	c.21-1662T>C		intron_variant				ENSP00000495987.1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91640 AN: 151748 Hom.: 28244 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.604 AC: 91706 AN: 151866 Hom.: 28273 Cov.: 31 AF XY: 0.601 AC XY: 44582 AN XY: 74222

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.618

Alfa AF: 0.527 Hom.: 1671

Bravo AF: 0.586

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.47

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: rs2237299; hg19: chr7-17347898;