dbSNP rs7258489: ENSG00000291145:n.1042G>A (chr19-46599884-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000594701.1(ENSG00000291145):n.1042G>A 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 0.282 in 152,166 control chromosomes in the GnomAD database, including 6,138 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 0.28 ( 6137 hom., cov: 32)

Exomes 𝑓: 0.35 ( 1 hom. )

Consequence

ENSG00000291145
ENST00000594701.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

Publications

9 publications found

Variant links:

Genes affected

ENSG00000291145 (HGNC:):

ENSG00000291145 links:

PPP5D1P (HGNC:44209): (PPP5 tetratricopeptide repeat domain containing 1, pseudogene)

PPP5D1P 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 (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP5D1P	NR_172902.1 link	n.34+999G>A		intron_variant	Intron 1 of 3
PPP5D1P	NR_172903.1 link	n.34+999G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291145	ENST00000594701.1 link	n.1042G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000291145	ENST00000414155.5 link	n.318+999G>A	intron_variant	Intron 1 of 3	2
ENSG00000291145	ENST00000593359.3 link	n.108+999G>A	intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42940

AN:

152022

Hom.:

6145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.302

GnomAD4 exome

AF:

0.346

AC:

AN:

Hom.:

Cov.:

AF XY:

0.438

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.429

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.282

AC:

42953

AN:

152140

Hom.:

6137

Cov.:

AF XY:

0.283

AC XY:

21019

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.268

AC:

11111

AN:

41496

American (AMR)

AF:

0.263

AC:

4017

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.402

AC:

1396

AN:

3472

East Asian (EAS)

AF:

0.101

AC:

525

AN:

5192

South Asian (SAS)

AF:

0.319

AC:

1540

AN:

4822

European-Finnish (FIN)

AF:

0.274

AC:

2906

AN:

10590

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.302

AC:

20492

AN:

67966

Other (OTH)

AF:

0.299

AC:

633

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1590

3180

4769

6359

7949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

444

888

1332

1776

2220

<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:

0.303

Hom.:

7620

Bravo

AF:

0.281

Asia WGS

AF:

0.192

AC:

666

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

1.9

(source)

DANN

Benign

0.59

PhyloP100

-2.1

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