dbSNP rs12053091: ENSG00000299339:n.405-32055T>C (chr2-112853203-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.288

Publications

9 publications found

Variant links:

COSMIC-nc: COSV57239635

Genes affected

ENSG00000299339 (HGNC:):

ENSG00000299339 links:

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

XIAPP3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299339	ENST00000762706.1 link	n.405-32055T>C	intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1 link	n.500-32055T>C	intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1 link	n.266-32055T>C	intron_variant	Intron 2 of 2

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

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1316

2632

3948

5264

6580

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

154

308

462

616

770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.261

AC:

39694

AN:

152152

Hom.:

5697

Cov.:

AF XY:

0.268

AC XY:

19918

AN XY:

74376

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.261

AC:

17755

AN:

67984

Other (OTH)

AF:

0.262

AC:

554

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1496

2993

4489

5986

7482

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.9

(source)

DANN

Benign

0.14

PhyloP100

0.29

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over