rs2040623

Variant summary

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

The NM_001621.5(AHR):​c.2403+810A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,006 control chromosomes in the GnomAD database, including 3,889 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 0.22 ( 3889 hom., cov: 32)

Consequence

AHR
NM_001621.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.475
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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AHRNM_001621.5 linkuse as main transcriptc.2403+810A>C intron_variant ENST00000242057.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AHRENST00000242057.9 linkuse as main transcriptc.2403+810A>C intron_variant 1 NM_001621.5 P2
AHRENST00000463496.1 linkuse as main transcriptc.2403+810A>C intron_variant, NMD_transcript_variant 1
AHRENST00000642825.1 linkuse as main transcriptc.2358+810A>C intron_variant A2

Frequencies

GnomAD3 genomes
AF:
0.216
AC:
32854
AN:
151890
Hom.:
3881
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.180
Gnomad AMI
AF:
0.146
Gnomad AMR
AF:
0.301
Gnomad ASJ
AF:
0.173
Gnomad EAS
AF:
0.413
Gnomad SAS
AF:
0.288
Gnomad FIN
AF:
0.169
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.210
Gnomad OTH
AF:
0.225
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.216
AC:
32876
AN:
152006
Hom.:
3889
Cov.:
32
AF XY:
0.218
AC XY:
16217
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.180
Gnomad4 AMR
AF:
0.303
Gnomad4 ASJ
AF:
0.173
Gnomad4 EAS
AF:
0.414
Gnomad4 SAS
AF:
0.286
Gnomad4 FIN
AF:
0.169
Gnomad4 NFE
AF:
0.210
Gnomad4 OTH
AF:
0.222
Alfa
AF:
0.216
Hom.:
5011
Bravo
AF:
0.228
Asia WGS
AF:
0.295
AC:
1024
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
12
DANN
Benign
0.86

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs2040623; hg19: chr7-17380662; API