11-67487072-C-G

Position:

• chr11-67487072-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001302959.2(AIP):​c.-12C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: AIP NM_001302959.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

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 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.37856337).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AIP	NM_003977.4	c.166C>G	p.Arg56Gly	missense_variant	2/6	ENST00000279146.8	NP_003968.3
AIP	NM_001302959.2	c.-12C>G		5_prime_UTR_premature_start_codon_gain_variant	2/6		NP_001289888.1
AIP	NM_001302960.2	c.166C>G	p.Arg56Gly	missense_variant	2/6		NP_001289889.1
AIP	NM_001302959.2	c.-12C>G		5_prime_UTR_variant	2/6		NP_001289888.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AIP	ENST00000279146.8	c.166C>G	p.Arg56Gly	missense_variant	2/6	1	NM_003977.4	ENSP00000279146.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Uncertain	0.034	T
BayesDel_noAF	Benign	-0.19
CADD	Benign	11
DANN	Uncertain	0.99
DEOGEN2	Benign	0.033	T;.
Eigen	Benign	-0.28
Eigen_PC	Benign	-0.32
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.29	T;T
M_CAP	Uncertain	0.21	D
MetaRNN	Benign	0.38	T;T
MetaSVM	Benign	-0.32	T
PrimateAI	Benign	0.32	T
PROVEAN	Benign	-1.9	N;N
REVEL	Uncertain	0.38
Sift	Benign	0.38	T;T
Sift4G	Benign	0.33	T;T
Vest4		0.28
MutPred		0.48		Loss of stability (P = 0.0215);Loss of stability (P = 0.0215);
MVP		0.84
MPC		0.71
ClinPred		0.81	D
GERP RS		3.3
gMVP		0.68

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

Other links and lift over

dbSNP: rs267606538; hg19: chr11-67254543;