chr10-109680961-T-A

Variant names:

• chr10-109680961-T-A
• rs7915504
• ENST00000603162.1:n.520T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
XIAPP1		n.109680961T>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XIAPP1	ENST00000603162.1	n.520T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.311 AC: 10198 AN: 32822

American (AMR) AF: 0.306 AC: 13639 AN: 44560

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 12401 AN: 25916

East Asian (EAS) AF: 0.235 AC: 9276 AN: 39552

South Asian (SAS) AF: 0.280 AC: 23979 AN: 85634

European-Finnish (FIN) AF: 0.528 AC: 28173 AN: 53380

Middle Eastern (MID) AF: 0.429 AC: 2446 AN: 5700

European-Non Finnish (NFE) AF: 0.502 AC: 542658 AN: 1081268

Other (OTH) AF: 0.451 AC: 26689 AN: 59202

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

African (AFR) AF: 0.318 AC: 13172 AN: 41452

American (AMR) AF: 0.363 AC: 5548 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1630 AN: 3458

East Asian (EAS) AF: 0.231 AC: 1191 AN: 5164

South Asian (SAS) AF: 0.267 AC: 1284 AN: 4818

European-Finnish (FIN) AF: 0.537 AC: 5685 AN: 10584

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33854 AN: 67920

Other (OTH) AF: 0.415 AC: 876 AN: 2112

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
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs7915504; hg19: chr10-111440719;