dbSNP rs12053091: XIAPP3:n.-125T>C (chr2-112853203-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000312918.2(XIAPP3):n.-125T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 298,888 control chromosomes in the GnomAD database, including 11,853 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 0.26 ( 5697 hom., cov: 32)

Exomes 𝑓: 0.27 ( 6156 hom. )

Consequence

XIAPP3
ENST00000312918.2 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.288

Variant links:

Genes affected

XIAPP3 (HGNC:52377): (X-linked inhibitor of apoptosis pseudogene 3)

XIAPP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

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
XIAPP3	ENST00000312918.2 link	n.-125T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39635

AN:

152034

Hom.:

5673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.403

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.261

Gnomad OTH

AF:

0.255

GnomAD4 exome

AF:

0.275

AC:

40334

AN:

146736

Hom.:

6156

AF XY:

0.280

AC XY:

22577

AN XY:

80636

show subpopulations

Gnomad4 AFR exome

AF:

0.157

Gnomad4 AMR exome

AF:

0.438

Gnomad4 ASJ exome

AF:

0.196

Gnomad4 EAS exome

AF:

0.378

Gnomad4 SAS exome

AF:

0.330

Gnomad4 FIN exome

AF:

0.291

Gnomad4 NFE exome

AF:

0.251

Gnomad4 OTH exome

AF:

0.263

GnomAD4 genome

AF:

0.261

AC:

39694

AN:

152152

Hom.:

5697

Cov.:

AF XY:

0.268

AC XY:

19918

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.404

Gnomad4 ASJ

AF:

0.188

Gnomad4 EAS

AF:

0.414

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.301

Gnomad4 NFE

AF:

0.261

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.260

Hom.:

7917

Bravo

AF:

0.265

Asia WGS

AF:

0.383

AC:

1333

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

2.9

DANN

Benign

0.14

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over