rs514324

Variant names:

• chr7-17054199-C-A
• rs514324
• ENST00000766380.1:n.632C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-17054199-C-A
• chr7-17054199-C-G

Variant summary

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

The ENST00000766380.1(ENSG00000289189):​n.632C>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 0.269 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: ENSG00000289189 ENST00000766380.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 0 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=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289189	ENST00000766380.1	n.632C>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000237773	ENST00000643090.1	n.307-82453G>T		intron_variant	Intron 2 of 2
AHR	ENST00000645559.1	n.30+137811C>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.383 AC: 15861 AN: 41446

American (AMR) AF: 0.214 AC: 3271 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3468

East Asian (EAS) AF: 0.0728 AC: 377 AN: 5178

South Asian (SAS) AF: 0.204 AC: 981 AN: 4818

European-Finnish (FIN) AF: 0.241 AC: 2542 AN: 10564

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16152 AN: 67950

Other (OTH) AF: 0.259 AC: 546 AN: 2110

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs514324; hg19: chr7-17093823;