rs2301677

Positions:

• chr7-17286434-T-C

Variant summary

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

The XR_007060234.1(LOC101927609):​n.581A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,020 control chromosomes in the GnomAD database, including 9,373 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 0.32 (9373 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC101927609 XR_007060234.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

LOC101927609 (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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927609	XR_007060234.1	n.581A>G		non_coding_transcript_exon_variant	4/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643090.1	n.229+12626A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48089 AN: 151902 Hom.: 9336 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.298

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.317 AC: 48188 AN: 152020 Hom.: 9373 Cov.: 32 AF XY: 0.314 AC XY: 23363 AN XY: 74302

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.295

Alfa AF: 0.238 Hom.: 6045

Bravo AF: 0.344

Asia WGS AF: 0.263 AC: 912 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2301677; hg19: chr7-17326058;