rs12053091

Variant names:

• chr2-112853203-T-C
• rs12053091
• ENST00000762706.1:n.405-32055T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000762706.1(ENSG00000299339):​n.405-32055T>C variant causes a intron 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: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 9 publications found

Genes affected

ENSG00000299339 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299339	ENST00000762706.1		n.405-32055T>C		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-32055T>C		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.266-32055T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39635 AN: 152034 Hom.: 5673 Cov.: 32

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

African (AFR) AF: 0.157 AC: 531 AN: 3388

American (AMR) AF: 0.438 AC: 2651 AN: 6050

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 743 AN: 3796

East Asian (EAS) AF: 0.378 AC: 2161 AN: 5720

South Asian (SAS) AF: 0.330 AC: 7826 AN: 23704

European-Finnish (FIN) AF: 0.291 AC: 1726 AN: 5930

Middle Eastern (MID) AF: 0.239 AC: 140 AN: 586

European-Non Finnish (NFE) AF: 0.251 AC: 22434 AN: 89508

Other (OTH) AF: 0.263 AC: 2122 AN: 8054

GnomAD4 genome AF: 0.261 AC: 39694 AN: 152152 Hom.: 5697 Cov.: 32 AF XY: 0.268 AC XY: 19918 AN XY: 74376

African (AFR) AF: 0.174 AC: 7247 AN: 41536

American (AMR) AF: 0.404 AC: 6178 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2138 AN: 5166

South Asian (SAS) AF: 0.358 AC: 1727 AN: 4828

European-Finnish (FIN) AF: 0.301 AC: 3176 AN: 10568

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17755 AN: 67984

Other (OTH) AF: 0.262 AC: 554 AN: 2116

Alfa AF: 0.263 Hom.: 18595

Bravo AF: 0.265

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.14
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs12053091; hg19: chr2-113610780; COSMIC: COSV57239635;