chr11-128942676-T-C

Position:

• chr11-128942676-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022112.3(TP53AIP1):​c.-77+118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 151,998 control chromosomes in the GnomAD database, including 31,848 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 0.64 (31848 hom., cov: 33)
  • Exomes 𝑓: 0.57 (30 hom.)
  • Failed GnomAD Quality Control
• Consequence: TP53AIP1 NM_022112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

TP53AIP1 (HGNC:29984): (tumor protein p53 regulated apoptosis inducing protein 1) This gene is specifically expressed in the thymus, and encodes a protein that is localized to the mitochondrion. The expression of this gene is inducible by p53, and it is thought to play an important role in mediating p53-dependent apoptosis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TP53AIP1	NM_022112.3	c.-77+118A>G		intron_variant		ENST00000531399.6	NP_071395.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TP53AIP1	ENST00000531399.6	c.-77+118A>G		intron_variant		1	NM_022112.3	ENSP00000432743	P2

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97125 AN: 151880 Hom.: 31793 Cov.: 33

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.684

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.572 AC: 87 AN: 152 Hom.: 30 AF XY: 0.609 AC XY: 67 AN XY: 110

Gnomad4 AFR exome AF: 0.833

Gnomad4 AMR exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.423

Gnomad4 NFE exome AF: 0.590

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.640 AC: 97237 AN: 151998 Hom.: 31848 Cov.: 33 AF XY: 0.637 AC XY: 47356 AN XY: 74286

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.688

Alfa AF: 0.605 Hom.: 28601

Bravo AF: 0.667

Asia WGS AF: 0.734 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.5
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2604235; hg19: chr11-128812571;