Genetic Variant ENPP7P14:n.5144954G>C (chr16-5144954-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.253 in 150,834 control chromosomes in the GnomAD database, including 5,271 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 0.25 ( 5271 hom., cov: 31)

Consequence

ENPP7P14
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

5 publications found

Variant links:

Genes affected

ENPP7P14 (HGNC:51387): (ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 14)

ENPP7P14 links:

ENSG00000285567 (HGNC:):

ENSG00000285567 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENPP7P14		n.5144954G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENPP7P14	ENST00000621765.1 link	n.252+3480C>G	intron_variant	Intron 1 of 2	6
ENSG00000285567	ENST00000650622.1 link	n.96+37187G>C	intron_variant	Intron 1 of 3
ENSG00000285567	ENST00000660079.1 link	n.119+37104G>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38191

AN:

150724

Hom.:

5277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.300

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.265

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.253

AC:

38178

AN:

150834

Hom.:

5271

Cov.:

AF XY:

0.252

AC XY:

18535

AN XY:

73602

show subpopulations

African (AFR)

AF:

0.144

AC:

5915

AN:

41064

American (AMR)

AF:

0.237

AC:

3587

AN:

15154

Ashkenazi Jewish (ASJ)

AF:

0.338

AC:

1172

AN:

3464

East Asian (EAS)

AF:

0.153

AC:

773

AN:

5046

South Asian (SAS)

AF:

0.300

AC:

1428

AN:

4764

European-Finnish (FIN)

AF:

0.299

AC:

3088

AN:

10316

Middle Eastern (MID)

AF:

0.313

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.315

AC:

21315

AN:

67734

Other (OTH)

AF:

0.264

AC:

554

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1386

2773

4159

5546

6932

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.164

Hom.:

353

Bravo

AF:

0.240

Asia WGS

AF:

0.231

AC:

806

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.78

(source)

DANN

Benign

0.065

PhyloP100

-1.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over