dbSNP rs2498804: ENSG00000307255:n.195G>T (chr14-104766758-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000824756.1(ENSG00000307255):n.195G>T 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 0.362 in 455,548 control chromosomes in the GnomAD database, including 32,073 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 0.34 ( 9104 hom., cov: 32)

Exomes 𝑓: 0.38 ( 22969 hom. )

Consequence

ENSG00000307255
ENST00000824756.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.800

Publications

62 publications found

Variant links:

Genes affected

ENSG00000307255 (HGNC:):

ENSG00000307255 links:

SIVA1 (HGNC:17712): (SIVA1 apoptosis inducing factor) This gene encodes an E3 ubiquitin ligase that regulates cell cycle progression, cell proliferation and apoptosis. The N-terminus of this protein binds to the cytoplasmic tail of the CD27 antigen, a member of the tumor necrosis factor receptor (TNFR) superfamily. In response to UV radiation-induced DNA damage, this protein has been shown to mediate the ubiquitination of proliferating cell nuclear antigen (PCNA), an important step in translesion DNA synthesis. [provided by RefSeq, Sep 2018]

SIVA1 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC102723342	XR_007064362.1 link	n.1944C>A	non_coding_transcript_exon_variant	Exon 1 of 2
LOC102723342	XR_429419.5 link	n.1944C>A	non_coding_transcript_exon_variant	Exon 1 of 3
LOC107987209	XR_001750914.3 link	n.107+85G>T	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307255	ENST00000824756.1 link	n.195G>T		non_coding_transcript_exon_variant	Exon 1 of 1
SIVA1	ENST00000553819.5 link	n.471-32C>A		intron_variant	Intron 3 of 5	3		ENSP00000451427.1		G3V3U1

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50919

AN:

151908

Hom.:

9105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.293

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.624

Gnomad SAS

AF:

0.515

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.332

GnomAD2 exomes

AF:

0.403

AC:

51497

AN:

127884

AF XY:

0.399

show subpopulations

Gnomad AFR exome

AF:

0.265

Gnomad AMR exome

AF:

0.507

Gnomad ASJ exome

AF:

0.280

Gnomad EAS exome

AF:

0.629

Gnomad FIN exome

AF:

0.358

Gnomad NFE exome

AF:

0.315

Gnomad OTH exome

AF:

0.361

GnomAD4 exome

AF:

0.376

AC:

114069

AN:

303522

Hom.:

22969

Cov.:

AF XY:

0.381

AC XY:

65852

AN XY:

172834

show subpopulations

African (AFR)

AF:

0.268

AC:

2308

AN:

8608

American (AMR)

AF:

0.505

AC:

13761

AN:

27252

Ashkenazi Jewish (ASJ)

AF:

0.285

AC:

3074

AN:

10784

East Asian (EAS)

AF:

0.624

AC:

5747

AN:

9204

South Asian (SAS)

AF:

0.466

AC:

27846

AN:

59700

European-Finnish (FIN)

AF:

0.363

AC:

4494

AN:

12364

Middle Eastern (MID)

AF:

0.371

AC:

1029

AN:

2776

European-Non Finnish (NFE)

AF:

0.320

AC:

50683

AN:

158628

Other (OTH)

AF:

0.361

AC:

5127

AN:

14206

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

3726

7452

11179

14905

18631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.335

AC:

50954

AN:

152026

Hom.:

9104

Cov.:

AF XY:

0.343

AC XY:

25479

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.268

AC:

11092

AN:

41462

American (AMR)

AF:

0.439

AC:

6703

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.286

AC:

991

AN:

3470

East Asian (EAS)

AF:

0.623

AC:

3224

AN:

5172

South Asian (SAS)

AF:

0.514

AC:

2472

AN:

4808

European-Finnish (FIN)

AF:

0.354

AC:

3737

AN:

10554

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.319

AC:

21662

AN:

67962

Other (OTH)

AF:

0.335

AC:

708

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1683

3366

5049

6732

8415

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

508

1016

1524

2032

2540

<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:

0.324

Hom.:

28767

Bravo

AF:

0.337

Asia WGS

AF:

0.562

AC:

1952

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.18

(source)

DANN

Benign

0.66

PhyloP100

-0.80

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