dbSNP rs2305779: PODNL1:c.651+34C>T (chr19-13934220-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.651+34C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,488,290 control chromosomes in the GnomAD database, including 12,713 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 0.10 ( 972 hom., cov: 33)

Exomes 𝑓: 0.13 ( 11741 hom. )

Consequence

PODNL1
NM_001370095.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.07

Publications

10 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:

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 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.651+34C>T	intron	N/A	NP_001357024.2	K7EPI2
PODNL1	NM_001146254.2		c.666+34C>T	intron	N/A	NP_001139726.1	Q6PEZ8-3
PODNL1	NM_024825.5		c.651+34C>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.651+34C>T	intron	N/A	ENSP00000467395.2	K7EPI2
PODNL1	ENST00000339560.10	TSL:1	c.651+34C>T	intron	N/A	ENSP00000345175.5	A0A2U3TZJ2
PODNL1	ENST00000886044.1		c.651+34C>T	intron	N/A	ENSP00000556103.1

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15801

AN:

152176

Hom.:

974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0342

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.0983

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.137

GnomAD2 exomes

AF:

0.120

AC:

14982

AN:

124554

AF XY:

0.121

show subpopulations

Gnomad AFR exome

AF:

0.0302

Gnomad AMR exome

AF:

0.0900

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.140

Gnomad NFE exome

AF:

0.115

Gnomad OTH exome

AF:

0.120

GnomAD4 exome

AF:

0.128

AC:

171087

AN:

1335996

Hom.:

11741

Cov.:

AF XY:

0.129

AC XY:

83920

AN XY:

651316

show subpopulations

African (AFR)

AF:

0.0303

AC:

917

AN:

30256

American (AMR)

AF:

0.0901

AC:

2144

AN:

23786

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

2908

AN:

19522

East Asian (EAS)

AF:

0.256

AC:

9638

AN:

37690

South Asian (SAS)

AF:

0.158

AC:

10498

AN:

66480

European-Finnish (FIN)

AF:

0.142

AC:

6378

AN:

44938

Middle Eastern (MID)

AF:

0.152

AC:

621

AN:

4082

European-Non Finnish (NFE)

AF:

0.124

AC:

130617

AN:

1053990

Other (OTH)

AF:

0.133

AC:

7366

AN:

55252

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

7360

14720

22080

29440

36800

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5004

10008

15012

20016

25020

<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:

0.104

AC:

15798

AN:

152294

Hom.:

972

Cov.:

AF XY:

0.105

AC XY:

7845

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0341

AC:

1416

AN:

41562

American (AMR)

AF:

0.0980

AC:

1499

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

497

AN:

3472

East Asian (EAS)

AF:

0.231

AC:

1197

AN:

5180

South Asian (SAS)

AF:

0.168

AC:

810

AN:

4832

European-Finnish (FIN)

AF:

0.147

AC:

1565

AN:

10612

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8384

AN:

68016

Other (OTH)

AF:

0.138

AC:

291

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

733

1466

2199

2932

3665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.116

Hom.:

1405

Bravo

AF:

0.0965

Asia WGS

AF:

0.190

AC:

659

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.088

(source)

DANN

Benign

0.61

PhyloP100

-3.1

PromoterAI

0.017

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over