dbSNP rs1540053: ENSG00000246090:n.3714+3418C>T (chr4-99160997-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 ENST00000500358.6(ENSG00000246090):n.3714+3418C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 190,614 control chromosomes in the GnomAD database, including 54,857 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 0.75 ( 42657 hom., cov: 32)

Exomes 𝑓: 0.79 ( 12200 hom. )

Consequence

ENSG00000246090
ENST00000500358.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.05

Publications

11 publications found

Variant links:

Genes affected

ENSG00000246090 (HGNC:):

ENSG00000246090 links:

PCNAP1 (HGNC:8732): (proliferating cell nuclear antigen pseudogene 1)

PCNAP1 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=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCNAP1	NR_028270.1 link	n.651G>A		non_coding_transcript_exon_variant	Exon 1 of 1
LOC100507053	NR_037884.1 link	n.3714+3418C>T		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000246090	ENST00000500358.6 link	n.3714+3418C>T	intron_variant	Intron 3 of 9	1
PCNAP1	ENST00000505363.2 link	n.649G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293361	ENST00000595299.1 link	n.269G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113251

AN:

151954

Hom.:

42641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.657

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.785

Gnomad ASJ

AF:

0.737

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.887

Gnomad FIN

AF:

0.728

Gnomad MID

AF:

0.822

Gnomad NFE

AF:

0.764

Gnomad OTH

AF:

0.751

GnomAD4 exome

AF:

0.794

AC:

30593

AN:

38542

Hom.:

12200

Cov.:

AF XY:

0.789

AC XY:

18264

AN XY:

23134

show subpopulations

African (AFR)

AF:

0.665

AC:

512

AN:

770

American (AMR)

AF:

0.838

AC:

4798

AN:

5728

Ashkenazi Jewish (ASJ)

AF:

0.741

AC:

461

AN:

622

East Asian (EAS)

AF:

0.999

AC:

2092

AN:

2094

South Asian (SAS)

AF:

0.864

AC:

3230

AN:

3740

European-Finnish (FIN)

AF:

0.713

AC:

2146

AN:

3008

Middle Eastern (MID)

AF:

0.771

AC:

833

AN:

1080

European-Non Finnish (NFE)

AF:

0.768

AC:

15364

AN:

20018

Other (OTH)

AF:

0.781

AC:

1157

AN:

1482

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

275

550

825

1100

1375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.745

AC:

113310

AN:

152072

Hom.:

42657

Cov.:

AF XY:

0.750

AC XY:

55750

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.656

AC:

27198

AN:

41452

American (AMR)

AF:

0.785

AC:

11982

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.737

AC:

2558

AN:

3470

East Asian (EAS)

AF:

0.998

AC:

5173

AN:

5182

South Asian (SAS)

AF:

0.888

AC:

4285

AN:

4826

European-Finnish (FIN)

AF:

0.728

AC:

7685

AN:

10562

Middle Eastern (MID)

AF:

0.818

AC:

239

AN:

292

European-Non Finnish (NFE)

AF:

0.764

AC:

51962

AN:

67996

Other (OTH)

AF:

0.753

AC:

1592

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1444

2888

4333

5777

7221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

852

1704

2556

3408

4260

<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:

0.760

Hom.:

132430

Bravo

AF:

0.743

Asia WGS

AF:

0.909

AC:

3160

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

4.2

(source)

DANN

Benign

0.45

PhyloP100

-2.1

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