rs7806681

chr7-17188498-C-T

Variant summary

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

The ENST00000643090.1(ENSG00000237773):n.306+70754G>A 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 0.528 in 151,802 control chromosomes in the GnomAD database, including 21,282 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 0.53 (21282 hom., cov: 32)
• Consequence: ENST00000643090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.604

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986772	XR_001745107.2	n.60-16205C>T		intron_variant, non_coding_transcript_variant
LOC101927609	XR_007060234.1	n.923-19907G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643090.1	n.306+70754G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80050 AN: 151684 Hom.: 21281 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.528 AC: 80094 AN: 151802 Hom.: 21282 Cov.: 32 AF XY: 0.526 AC XY: 39014 AN XY: 74186

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.560

Alfa AF: 0.543 Hom.: 17445

Bravo AF: 0.530

Asia WGS AF: 0.595 AC: 2069 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.7
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7806681; hg19: chr7-17228122;