11-67482759-GTTT-GTTTT

Variant names:

• chr11-67482759-G-GT
• rs201817175
• ENST00000682699.1:c.-366-34_-366-33insT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000682699.1(AIP):​c.-366-34_-366-33insT 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
• Publications: 0 publications found

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]

AIP Gene-Disease associations (from GenCC):

• growth hormone secreting pituitary adenoma 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• familial isolated pituitary adenoma

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• pituitary gigantism

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• acromegaly

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000682699.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AIP	ENST00000682699.1		c.-366-34_-366-33insT		intron	N/A	ENSP00000507935.1	A0A804HKH9

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

African (AFR) AF: 0.0821 AC: 2934 AN: 35756

American (AMR) AF: 0.00970 AC: 126 AN: 12988

Ashkenazi Jewish (ASJ) AF: 0.00195 AC: 6 AN: 3074

East Asian (EAS) AF: 0.00402 AC: 18 AN: 4478

South Asian (SAS) AF: 0.00381 AC: 15 AN: 3936

European-Finnish (FIN) AF: 0.0179 AC: 139 AN: 7758

Middle Eastern (MID) AF: 0.00382 AC: 1 AN: 262

European-Non Finnish (NFE) AF: 0.00290 AC: 173 AN: 59676

Other (OTH) AF: 0.0219 AC: 39 AN: 1778

Alfa AF: 0.000567 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs201817175; hg19: chr11-67250230; COSMIC: COSV54159896;