rs847428

Variant names:

• chr7-16990328-C-A
• rs847428
• ENST00000685941.3:n.212C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-16990328-C-A
• chr7-16990328-C-G
• chr7-16990328-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685941.3(ENSG00000289189):​n.212C>A 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 0.117 in 152,222 control chromosomes in the GnomAD database, including 1,373 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 0.12 (1373 hom., cov: 32)
• Consequence: ENSG00000289189 ENST00000685941.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 1 publications found

Genes affected

ENSG00000289189 (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]

AHR Gene-Disease associations (from GenCC):

• retinitis pigmentosa 85

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• retinitis pigmentosa

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• foveal hypoplasia

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375170	XR_007060237.1	n.111C>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105375170	XR_007060238.1	n.111C>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124901595	XR_007060239.1	n.13494G>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105375170	XR_927067.3	n.111C>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289189	ENST00000685941.3	n.212C>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000289189	ENST00000687986.3	n.267C>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289189	ENST00000766378.1	n.205C>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17743 AN: 152104 Hom.: 1372 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.117 AC: 17746 AN: 152222 Hom.: 1373 Cov.: 32 AF XY: 0.117 AC XY: 8707 AN XY: 74414

African (AFR) AF: 0.0293 AC: 1216 AN: 41556

American (AMR) AF: 0.130 AC: 1989 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 411 AN: 3470

East Asian (EAS) AF: 0.0396 AC: 205 AN: 5176

South Asian (SAS) AF: 0.0737 AC: 356 AN: 4830

European-Finnish (FIN) AF: 0.184 AC: 1950 AN: 10572

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11170 AN: 68008

Other (OTH) AF: 0.107 AC: 226 AN: 2114

Alfa AF: 0.0907 Hom.: 166

Bravo AF: 0.108

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.1
DANN	Benign	0.57
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs847428; hg19: chr7-17029952;