dbSNP rs2305778: PODNL1:c.768-19C>T (chr19-13933474-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001370095.3(PODNL1):c.768-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 1,533,248 control chromosomes in the GnomAD database, including 4,235 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 0.056 ( 304 hom., cov: 33)

Exomes 𝑓: 0.071 ( 3931 hom. )

Consequence

PODNL1
NM_001370095.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219

Publications

8 publications found

Variant links:

Genes affected

PODNL1 (HGNC:26275): (podocan like 1) Predicted to be located in collagen-containing extracellular matrix. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

PODNL1 links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370095.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PODNL1	NM_001370095.3	MANE Select	c.768-19C>T	intron	N/A	NP_001357024.2	K7EPI2
PODNL1	NM_001146254.2		c.783-19C>T	intron	N/A	NP_001139726.1	Q6PEZ8-3
PODNL1	NM_024825.5		c.768-19C>T	intron	N/A	NP_079101.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PODNL1	ENST00000588872.3	TSL:3 MANE Select	c.768-19C>T	intron	N/A	ENSP00000467395.2	K7EPI2
PODNL1	ENST00000339560.10	TSL:1	c.768-19C>T	intron	N/A	ENSP00000345175.5	A0A2U3TZJ2
PODNL1	ENST00000886044.1		c.768-19C>T	intron	N/A	ENSP00000556103.1

Frequencies

GnomAD3 genomes

AF:

0.0561

AC:

8530

AN:

152116

Hom.:

304

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0114

Gnomad AMI

AF:

0.0571

Gnomad AMR

AF:

0.0513

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.108

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.0905

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0674

Gnomad OTH

AF:

0.0604

GnomAD2 exomes

AF:

0.0772

AC:

14611

AN:

189162

AF XY:

0.0818

show subpopulations

Gnomad AFR exome

AF:

0.0100

Gnomad AMR exome

AF:

0.0501

Gnomad ASJ exome

AF:

0.126

Gnomad EAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.0956

Gnomad NFE exome

AF:

0.0697

Gnomad OTH exome

AF:

0.0828

GnomAD4 exome

AF:

0.0715

AC:

98690

AN:

1381014

Hom.:

3931

Cov.:

AF XY:

0.0735

AC XY:

49899

AN XY:

678834

show subpopulations

African (AFR)

AF:

0.0115

AC:

367

AN:

31800

American (AMR)

AF:

0.0494

AC:

1809

AN:

36600

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

2473

AN:

22098

East Asian (EAS)

AF:

0.108

AC:

4201

AN:

38846

South Asian (SAS)

AF:

0.131

AC:

10054

AN:

76544

European-Finnish (FIN)

AF:

0.0949

AC:

3552

AN:

37420

Middle Eastern (MID)

AF:

0.0846

AC:

461

AN:

5448

European-Non Finnish (NFE)

AF:

0.0666

AC:

71573

AN:

1074914

Other (OTH)

AF:

0.0732

AC:

4200

AN:

57344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

4597

9194

13792

18389

22986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2782

5564

8346

11128

13910

<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:

0.0560

AC:

8530

AN:

152234

Hom.:

304

Cov.:

AF XY:

0.0582

AC XY:

4330

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0114

AC:

475

AN:

41554

American (AMR)

AF:

0.0511

AC:

782

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

369

AN:

3466

East Asian (EAS)

AF:

0.108

AC:

557

AN:

5158

South Asian (SAS)

AF:

0.125

AC:

603

AN:

4830

European-Finnish (FIN)

AF:

0.0905

AC:

960

AN:

10610

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0674

AC:

4582

AN:

68010

Other (OTH)

AF:

0.0617

AC:

130

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

420

840

1260

1680

2100

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0656

Hom.:

659

Bravo

AF:

0.0496

Asia WGS

AF:

0.0960

AC:

334

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.6

(source)

DANN

Benign

0.42

PhyloP100

0.22

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over