Genetic Variant POPDC3:c.-252+2887C>G (chr6-105176946-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 NM_022361.5(POPDC3):c.-252+2887C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 162,264 control chromosomes in the GnomAD database, including 43,883 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 0.68 ( 40667 hom., cov: 33)

Exomes 𝑓: 0.79 ( 3216 hom. )

Consequence

POPDC3
NM_022361.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364

Publications

1 publications found

Variant links:

Genes affected

POPDC3 (HGNC:17649): (popeye domain containing 3) This gene encodes a member of the POP family of proteins containing three putative transmembrane domains. This gene is expressed in cardiac and skeletal muscle and may play an important role in these tissues during development. Alternatively spliced transcript variants have been found. [provided by RefSeq, Nov 2008]

POPDC3 links:

BVES-AS1 (HGNC:21223): (BVES antisense RNA 1)

BVES-AS1 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POPDC3	NM_022361.5 link	c.-252+2887C>G		intron_variant	Intron 1 of 3	ENST00000254765.4	NP_071756.2	Q9HBV1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POPDC3	ENST00000254765.4 link	c.-252+2887C>G		intron_variant	Intron 1 of 3	1	NM_022361.5	ENSP00000254765.3		Q9HBV1

Frequencies

GnomAD3 genomes

AF:

0.676

AC:

102729

AN:

152052

Hom.:

40661

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.955

Gnomad AMR

AF:

0.814

Gnomad ASJ

AF:

0.824

Gnomad EAS

AF:

0.878

Gnomad SAS

AF:

0.822

Gnomad FIN

AF:

0.878

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.849

Gnomad OTH

AF:

0.728

GnomAD4 exome

AF:

0.791

AC:

7982

AN:

10096

Hom.:

3216

Cov.:

AF XY:

0.788

AC XY:

3938

AN XY:

4996

show subpopulations

African (AFR)

AF:

0.0991

AC:

AN:

232

American (AMR)

AF:

0.900

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.759

AC:

AN:

East Asian (EAS)

AF:

0.741

AC:

AN:

South Asian (SAS)

AF:

0.759

AC:

126

AN:

166

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.450

AC:

AN:

European-Non Finnish (NFE)

AF:

0.810

AC:

7479

AN:

9232

Other (OTH)

AF:

0.782

AC:

247

AN:

316

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

156

235

313

391

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

236

472

708

944

1180

<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:

0.675

AC:

102739

AN:

152168

Hom.:

40667

Cov.:

AF XY:

0.681

AC XY:

50657

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.224

AC:

9277

AN:

41472

American (AMR)

AF:

0.814

AC:

12446

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.824

AC:

2858

AN:

3468

East Asian (EAS)

AF:

0.878

AC:

4553

AN:

5184

South Asian (SAS)

AF:

0.823

AC:

3968

AN:

4824

European-Finnish (FIN)

AF:

0.878

AC:

9303

AN:

10592

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.848

AC:

57714

AN:

68020

Other (OTH)

AF:

0.730

AC:

1544

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1132

2265

3397

4530

5662

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<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:

0.742

Hom.:

5486

Bravo

AF:

0.652

Asia WGS

AF:

0.824

AC:

2865

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.9

(source)

DANN

Benign

0.73

PhyloP100

-0.36

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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