chr11-67482759-GT-G

Variant names:

• chr11-67482759-GT-G
• rs201817175
• ENST00000682699.1:c.-366-33delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000682699.1(AIP):​c.-366-33delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 130,666 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0013 (0 hom., cov: 28)
• Consequence: AIP ENST00000682699.1 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00131 (171/130666) while in subpopulation SAS AF= 0.00229 (9/3938). AF 95% confidence interval is 0.00119. There are 0 homozygotes in gnomad4. There are 90 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 171 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AIP	ENST00000682699.1	c.-366-33delT		intron_variant	Intron 2 of 7			ENSP00000507935.1

Frequencies

GnomAD3 genomes AF: 0.00130 AC: 170 AN: 130672 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.000812

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00325

Gnomad EAS AF: 0.000445

Gnomad SAS AF: 0.00227

Gnomad FIN AF: 0.00322

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00125

Gnomad OTH AF: 0.00169

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

GnomAD4 genome AF: 0.00131 AC: 171 AN: 130666 Hom.: 0 Cov.: 28 AF XY: 0.00143 AC XY: 90 AN XY: 62840

Gnomad4 AFR AF: 0.000839

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.00325

Gnomad4 EAS AF: 0.000446

Gnomad4 SAS AF: 0.00229

Gnomad4 FIN AF: 0.00322

Gnomad4 NFE AF: 0.00126

Gnomad4 OTH AF: 0.00169

ClinVar

Not reported in ClinVar

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;