rs514324

chr7-17054199-C-Achr7-17054199-C-G

Variant summary

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

The ENST00000643090.1(ENSG00000237773):n.307-82453G>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 0.269 in 152,024 control chromosomes in the GnomAD database, including 6,049 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 0.27 (6049 hom., cov: 32)
• Consequence: ENST00000643090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643090.1	n.307-82453G>T		intron_variant, non_coding_transcript_variant
AHR	ENST00000645559.1	n.30+137811C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40797 AN: 151906 Hom.: 6037 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.269 AC: 40845 AN: 152024 Hom.: 6049 Cov.: 32 AF XY: 0.265 AC XY: 19669 AN XY: 74296

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.259

Alfa AF: 0.202 Hom.: 892

Bravo AF: 0.271

Asia WGS AF: 0.153 AC: 534 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	1.1
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs514324; hg19: chr7-17093823;