dbSNP rs6438759: PARP14:n.3801A>G (chr3-122721219-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000474669.1(PARP14):n.3801A>G 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 0.889 in 233,872 control chromosomes in the GnomAD database, including 92,558 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 0.89 ( 59770 hom., cov: 31)

Exomes 𝑓: 0.89 ( 32788 hom. )

Consequence

PARP14
ENST00000474669.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318

Publications

3 publications found

Variant links:

Genes affected

PARP14 (HGNC:29232): (poly(ADP-ribose) polymerase family member 14) This gene encodes a member of the poly(ADP-ribose) polymerase (PARP) protein family. The encoded anti-apoptotic protein may regulate aerobic glycolysis and promote survival of cancer cells. Increased expression of this gene has been reported in a variety of tumor types. [provided by RefSeq, Jul 2016]

PARP14 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARP14	NM_017554.3 link	c.4941+831A>G		intron_variant	Intron 15 of 16	ENST00000474629.7	NP_060024.2	Q460N5-6Q8N546
PARP14	XR_007095695.1 link	n.5118A>G		non_coding_transcript_exon_variant	Exon 16 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARP14	ENST00000474629.7 link	c.4941+831A>G		intron_variant	Intron 15 of 16	1	NM_017554.3	ENSP00000418194.2		Q460N5-6

Frequencies

GnomAD3 genomes

AF:

0.886

AC:

134744

AN:

152050

Hom.:

59715

Cov.:

show subpopulations

Gnomad AFR

AF:

0.868

Gnomad AMI

AF:

0.943

Gnomad AMR

AF:

0.914

Gnomad ASJ

AF:

0.883

Gnomad EAS

AF:

0.982

Gnomad SAS

AF:

0.949

Gnomad FIN

AF:

0.878

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.880

Gnomad OTH

AF:

0.885

GnomAD4 exome

AF:

0.895

AC:

73122

AN:

81704

Hom.:

32788

Cov.:

AF XY:

0.900

AC XY:

40085

AN XY:

44518

show subpopulations

African (AFR)

AF:

0.860

AC:

425

AN:

494

American (AMR)

AF:

0.921

AC:

3262

AN:

3542

Ashkenazi Jewish (ASJ)

AF:

0.887

AC:

1433

AN:

1616

East Asian (EAS)

AF:

0.981

AC:

1322

AN:

1348

South Asian (SAS)

AF:

0.937

AC:

15611

AN:

16662

European-Finnish (FIN)

AF:

0.875

AC:

3635

AN:

4154

Middle Eastern (MID)

AF:

0.892

AC:

257

AN:

288

European-Non Finnish (NFE)

AF:

0.879

AC:

43542

AN:

49528

Other (OTH)

AF:

0.893

AC:

3635

AN:

4072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

358

716

1074

1432

1790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

214

428

642

856

1070

<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:

0.886

AC:

134858

AN:

152168

Hom.:

59770

Cov.:

AF XY:

0.888

AC XY:

66039

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.868

AC:

35996

AN:

41478

American (AMR)

AF:

0.914

AC:

13984

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.883

AC:

3066

AN:

3472

East Asian (EAS)

AF:

0.982

AC:

5083

AN:

5176

South Asian (SAS)

AF:

0.949

AC:

4582

AN:

4828

European-Finnish (FIN)

AF:

0.878

AC:

9303

AN:

10594

Middle Eastern (MID)

AF:

0.881

AC:

259

AN:

294

European-Non Finnish (NFE)

AF:

0.880

AC:

59856

AN:

68006

Other (OTH)

AF:

0.886

AC:

1869

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

788

1576

2365

3153

3941

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

904

1808

2712

3616

4520

<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:

0.888

Hom.:

30619

Bravo

AF:

0.888

Asia WGS

AF:

0.956

AC:

3326

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

5.2

(source)

DANN

Benign

0.65

PhyloP100

0.32

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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