chr7-17286434-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000642825.1(AHR):​c.-202-9863T>C variant causes a intron 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

AHR
ENST00000642825.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.152
Variant links:
Genes affected
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]

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ACMG classification

Classification made for transcript

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 Protein UniProt
LOC101927609XR_007060230.1 linkn.445A>G non_coding_transcript_exon_variant 4/6
LOC101927609XR_007060231.1 linkn.303A>G non_coding_transcript_exon_variant 3/5
LOC101927609XR_007060232.1 linkn.303A>G non_coding_transcript_exon_variant 3/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AHRENST00000642825.1 linkc.-202-9863T>C intron_variant ENSP00000495987.1 A0A2R8Y7G1
ENSG00000237773ENST00000415246.2 linkn.445A>G non_coding_transcript_exon_variant 4/43
ENSG00000237773ENST00000419382.6 linkn.237A>G non_coding_transcript_exon_variant 2/43

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2301677; hg19: chr7-17326058; API