rs3757824

chr7-17296411-T-Cchr7-17296411-T-G

Variant summary

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

The ENST00000643090.1(ENSG00000237773):n.229+2649A>G 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 0.217 in 384,698 control chromosomes in the GnomAD database, including 9,789 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 0.21 (3557 hom., cov: 31)
  • Exomes 𝑓: 0.22 (6232 hom.)
• Consequence: ENST00000643090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927609	XR_007060234.1	n.262-1151A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643090.1	n.229+2649A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31631 AN: 151676 Hom.: 3548 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.222 AC: 51683 AN: 232904 Hom.: 6232 Cov.: 0 AF XY: 0.222 AC XY: 26242 AN XY: 118182

Gnomad4 AFR exome AF: 0.172

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.344

Gnomad4 SAS exome AF: 0.289

Gnomad4 FIN exome AF: 0.158

Gnomad4 NFE exome AF: 0.210

Gnomad4 OTH exome AF: 0.226

GnomAD4 genome AF: 0.209 AC: 31650 AN: 151794 Hom.: 3557 Cov.: 31 AF XY: 0.209 AC XY: 15544 AN XY: 74202

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.219

Alfa AF: 0.208 Hom.: 6018

Bravo AF: 0.220

Asia WGS AF: 0.249 AC: 864 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.028
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: rs3757824; hg19: chr7-17336035;