rs6960165

Positions:

• chr7-17328461-G-A
• chr7-17328461-G-C
• chr7-17328461-G-T

Variant summary

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

The NM_001621.5(AHR):​c.450+613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 151,848 control chromosomes in the GnomAD database, including 50,648 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 0.81 (50648 hom., cov: 32)
• Consequence: AHR NM_001621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHR	NM_001621.5	c.450+613G>A		intron_variant		ENST00000242057.9	NP_001612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHR	ENST00000242057.9	c.450+613G>A		intron_variant		1	NM_001621.5	ENSP00000242057	P2
AHR	ENST00000463496.1	c.450+613G>A		intron_variant, NMD_transcript_variant		1		ENSP00000436466
AHR	ENST00000642825.1	c.405+613G>A		intron_variant				ENSP00000495987	A2

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123147 AN: 151730 Hom.: 50589 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.812 AC: 123263 AN: 151848 Hom.: 50648 Cov.: 32 AF XY: 0.813 AC XY: 60327 AN XY: 74238

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.796

Alfa AF: 0.768 Hom.: 71302

Bravo AF: 0.810

Asia WGS AF: 0.803 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.39

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: rs6960165; hg19: chr7-17368085;