rs6555205

Positions:

Variant summary

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

The NM_001377236.1(AHRR):​c.244+6517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,082 control chromosomes in the GnomAD database, including 19,933 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 0.51 ( 19933 hom., cov: 33)

Consequence

AHRR
NM_001377236.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.442
Variant links:
Genes affected
AHRR (HGNC:346): (aryl hydrocarbon receptor repressor) The protein encoded by this gene participates in the aryl hydrocarbon receptor (AhR) signaling cascade, which mediates dioxin toxicity, and is involved in regulation of cell growth and differentiation. It functions as a feedback modulator by repressing AhR-dependent gene expression. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jun 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AHRRNM_001377236.1 linkuse as main transcriptc.244+6517C>T intron_variant ENST00000684583.1
PDCD6-AHRRNR_165159.2 linkuse as main transcriptn.537+6517C>T intron_variant, non_coding_transcript_variant
AHRRNM_001377239.1 linkuse as main transcriptc.244+6517C>T intron_variant
PDCD6-AHRRNR_165163.2 linkuse as main transcriptn.537+6517C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AHRRENST00000684583.1 linkuse as main transcriptc.244+6517C>T intron_variant NM_001377236.1 P1

Frequencies

GnomAD3 genomes
AF:
0.508
AC:
77228
AN:
151964
Hom.:
19926
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.520
Gnomad AMI
AF:
0.411
Gnomad AMR
AF:
0.462
Gnomad ASJ
AF:
0.486
Gnomad EAS
AF:
0.278
Gnomad SAS
AF:
0.524
Gnomad FIN
AF:
0.472
Gnomad MID
AF:
0.475
Gnomad NFE
AF:
0.536
Gnomad OTH
AF:
0.502
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.508
AC:
77265
AN:
152082
Hom.:
19933
Cov.:
33
AF XY:
0.504
AC XY:
37475
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.520
Gnomad4 AMR
AF:
0.462
Gnomad4 ASJ
AF:
0.486
Gnomad4 EAS
AF:
0.279
Gnomad4 SAS
AF:
0.524
Gnomad4 FIN
AF:
0.472
Gnomad4 NFE
AF:
0.536
Gnomad4 OTH
AF:
0.506
Alfa
AF:
0.530
Hom.:
34249
Bravo
AF:
0.504
Asia WGS
AF:
0.402
AC:
1399
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.1
DANN
Benign
0.74

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: rs6555205; hg19: chr5-360543; API