rs7915504

chr10-109680961-T-Achr10-109680961-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000603162.1(XIAPP1):n.520T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,580,022 control chromosomes in the GnomAD database, including 176,256 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 0.42 (14244 hom., cov: 32)
  • Exomes 𝑓: 0.47 (162012 hom.)
• Consequence: XIAPP1 ENST00000603162.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.46

Genes affected

XIAPP1 (HGNC:52375): (X-linked inhibitor of apoptosis pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XIAPP1	ENST00000603162.1	n.520T>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63927 AN: 151870 Hom.: 14249 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.420

GnomAD4 exome AF: 0.469 AC: 669459 AN: 1428034 Hom.: 162012 Cov.: 34 AF XY: 0.464 AC XY: 330554 AN XY: 712240

Gnomad4 AFR exome AF: 0.311

Gnomad4 AMR exome AF: 0.306

Gnomad4 ASJ exome AF: 0.479

Gnomad4 EAS exome AF: 0.235

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.528

Gnomad4 NFE exome AF: 0.502

Gnomad4 OTH exome AF: 0.451

GnomAD4 genome AF: 0.421 AC: 63926 AN: 151988 Hom.: 14244 Cov.: 32 AF XY: 0.415 AC XY: 30832 AN XY: 74294

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.415

Alfa AF: 0.467 Hom.: 2084

Bravo AF: 0.406

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
Cadd	Benign	3.7
Dann	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7915504; hg19: chr10-111440719;