7-17293365-C-T

Position:

• chr7-17293365-C-T

Variant summary

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

The ENST00000643090.1(ENSG00000237773):​n.229+5695G>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 0.788 in 151,948 control chromosomes in the GnomAD database, including 47,564 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 0.79 (47564 hom., cov: 30)
• Consequence: ENST00000643090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927609	XR_007060234.1	n.356+1801G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643090.1	n.229+5695G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119581 AN: 151830 Hom.: 47530 Cov.: 30

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.788 AC: 119669 AN: 151948 Hom.: 47564 Cov.: 30 AF XY: 0.785 AC XY: 58308 AN XY: 74258

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.780

Alfa AF: 0.762 Hom.: 42462

Bravo AF: 0.786

Asia WGS AF: 0.682 AC: 2371 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
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: rs10250822; hg19: chr7-17332989;