11-67482759-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000682699.1(AIP):c.-366-20dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0264 in 130,536 control chromosomes in the GnomAD database, including 114 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.026 (114 hom., cov: 28)
• Consequence: AIP ENST00000682699.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.57

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-67482759-G-GT is Benign according to our data. Variant chr11-67482759-G-GT is described in ClinVar as [Benign]. Clinvar id is 1234779.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AIP	ENST00000682699.1	c.-366-20dup		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 3449 AN: 130540 Hom.: 114 Cov.: 28

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.00120

Gnomad AMR AF: 0.00978

Gnomad ASJ AF: 0.00195

Gnomad EAS AF: 0.00400

Gnomad SAS AF: 0.00404

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.00347

Gnomad NFE AF: 0.00290

Gnomad OTH AF: 0.0220

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0264 AC: 3452 AN: 130536 Hom.: 114 Cov.: 28 AF XY: 0.0260 AC XY: 1632 AN XY: 62768

Gnomad4 AFR AF: 0.0821

Gnomad4 AMR AF: 0.00970

Gnomad4 ASJ AF: 0.00195

Gnomad4 EAS AF: 0.00402

Gnomad4 SAS AF: 0.00381

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.00290

Gnomad4 OTH AF: 0.0219

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 19, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201817175; hg19: chr11-67250230;