rs1523632

Positions:

• chr7-17030344-G-A

Variant summary

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

The ENST00000643090.1(ENSG00000237773):​n.307-58598C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,058 control chromosomes in the GnomAD database, including 19,585 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 0.48 (19585 hom., cov: 33)
• Consequence: ENST00000643090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

Genes affected

(HGNC:):

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901595	XR_007060239.1	n.13339+5344C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643090.1	n.307-58598C>T		intron_variant, non_coding_transcript_variant
AHR	ENST00000645559.1	n.30+113956G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73687 AN: 151940 Hom.: 19578 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.485 AC: 73697 AN: 152058 Hom.: 19585 Cov.: 33 AF XY: 0.492 AC XY: 36559 AN XY: 74340

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.471

Alfa AF: 0.548 Hom.: 46515

Bravo AF: 0.480

Asia WGS AF: 0.505 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1523632; hg19: chr7-17069968;