11-67479201-C-T

Variant summary

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

The ENST00000682699.1(AIP):​c.-367+2003C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,554 control chromosomes in the GnomAD database, including 3,378 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 ( 3378 hom., cov: 30)

Consequence

AIP
ENST00000682699.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.145
Variant links:
Genes affected
AIP (HGNC:358): (aryl hydrocarbon receptor interacting protein) The protein encoded by this gene is a receptor for aryl hydrocarbons and a ligand-activated transcription factor. The encoded protein is found in the cytoplasm as part of a multiprotein complex, but upon binding of ligand is transported to the nucleus. This protein can regulate the expression of many xenobiotic metabolizing enzymes. Also, the encoded protein can bind specifically to and inhibit the activity of hepatitis B virus. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]

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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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.67479201C>T intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AIPENST00000682699.1 linkuse as main transcriptc.-367+2003C>T intron_variant ENSP00000507935.1 A0A804HKH9

Frequencies

GnomAD3 genomes
AF:
0.116
AC:
17626
AN:
151460
Hom.:
3377
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.401
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0506
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00146
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.00233
Gnomad OTH
AF:
0.0885
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.116
AC:
17643
AN:
151554
Hom.:
3378
Cov.:
30
AF XY:
0.111
AC XY:
8230
AN XY:
74032
show subpopulations
Gnomad4 AFR
AF:
0.400
Gnomad4 AMR
AF:
0.0504
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00125
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00233
Gnomad4 OTH
AF:
0.0878
Alfa
AF:
0.00491
Hom.:
15
Bravo
AF:
0.131
Asia WGS
AF:
0.0170
AC:
61
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.96
DANN
Benign
0.67

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: rs2514259; hg19: chr11-67246672; API