rs5064

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006172.4(NPPA):​c.123+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 1,614,006 control chromosomes in the GnomAD database, including 8,829 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 2084 hom., cov: 32)
Exomes 𝑓: 0.088 ( 6745 hom. )

Consequence

NPPA
NM_006172.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.517
Variant links:
Genes affected
NPPA (HGNC:7939): (natriuretic peptide A) The protein encoded by this gene belongs to the natriuretic peptide family. Natriuretic peptides are implicated in the control of extracellular fluid volume and electrolyte homeostasis. This protein is synthesized as a large precursor (containing a signal peptide), which is processed to release a peptide from the N-terminus with similarity to vasoactive peptide, cardiodilatin, and another peptide from the C-terminus with natriuretic-diuretic activity. Mutations in this gene have been associated with atrial fibrillation familial type 6. This gene is located adjacent to another member of the natriuretic family of peptides on chromosome 1. [provided by RefSeq, Oct 2015]
CLCN6 (HGNC:2024): (chloride voltage-gated channel 6) This gene encodes a member of the voltage-dependent chloride channel protein family. Members of this family can function as either chloride channels or antiporters. This protein is primarily localized to late endosomes and functions as a chloride/proton antiporter. Alternate splicing results in both coding and non-coding variants. Additional alternately spliced variants have been described but their full-length structure is unknown. [provided by RefSeq, Mar 2012]
NPPA-AS1 (HGNC:37635): (NPPA antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 1-11847546-G-A is Benign according to our data. Variant chr1-11847546-G-A is described in ClinVar as [Benign]. Clinvar id is 36663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-11847546-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NPPANM_006172.4 linkc.123+16C>T intron_variant Intron 1 of 2 ENST00000376480.7 NP_006163.1 P01160
NPPA-AS1NR_037806.1 linkn.1592G>A non_coding_transcript_exon_variant Exon 4 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NPPAENST00000376480.7 linkc.123+16C>T intron_variant Intron 1 of 2 1 NM_006172.4 ENSP00000365663.3 P01160

Frequencies

GnomAD3 genomes
AF:
0.135
AC:
20525
AN:
152070
Hom.:
2084
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.284
Gnomad AMI
AF:
0.0987
Gnomad AMR
AF:
0.0895
Gnomad ASJ
AF:
0.0518
Gnomad EAS
AF:
0.00675
Gnomad SAS
AF:
0.0960
Gnomad FIN
AF:
0.0405
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.0863
Gnomad OTH
AF:
0.136
GnomAD2 exomes
AF:
0.0857
AC:
21539
AN:
251394
AF XY:
0.0840
show subpopulations
Gnomad AFR exome
AF:
0.290
Gnomad AMR exome
AF:
0.0586
Gnomad ASJ exome
AF:
0.0605
Gnomad EAS exome
AF:
0.00772
Gnomad FIN exome
AF:
0.0437
Gnomad NFE exome
AF:
0.0808
Gnomad OTH exome
AF:
0.0875
GnomAD4 exome
AF:
0.0875
AC:
127941
AN:
1461818
Hom.:
6745
Cov.:
33
AF XY:
0.0883
AC XY:
64213
AN XY:
727202
show subpopulations
African (AFR)
AF:
0.292
AC:
9764
AN:
33476
American (AMR)
AF:
0.0615
AC:
2749
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
0.0617
AC:
1613
AN:
26136
East Asian (EAS)
AF:
0.00461
AC:
183
AN:
39700
South Asian (SAS)
AF:
0.110
AC:
9476
AN:
86252
European-Finnish (FIN)
AF:
0.0428
AC:
2285
AN:
53412
Middle Eastern (MID)
AF:
0.135
AC:
776
AN:
5768
European-Non Finnish (NFE)
AF:
0.0859
AC:
95490
AN:
1111954
Other (OTH)
AF:
0.0928
AC:
5605
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.477
Heterozygous variant carriers
0
7404
14807
22211
29614
37018
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
3616
7232
10848
14464
18080
<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:
0.135
AC:
20534
AN:
152188
Hom.:
2084
Cov.:
32
AF XY:
0.132
AC XY:
9826
AN XY:
74414
show subpopulations
African (AFR)
AF:
0.284
AC:
11769
AN:
41466
American (AMR)
AF:
0.0893
AC:
1367
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
0.0518
AC:
180
AN:
3472
East Asian (EAS)
AF:
0.00677
AC:
35
AN:
5172
South Asian (SAS)
AF:
0.0959
AC:
463
AN:
4828
European-Finnish (FIN)
AF:
0.0405
AC:
430
AN:
10610
Middle Eastern (MID)
AF:
0.160
AC:
47
AN:
294
European-Non Finnish (NFE)
AF:
0.0863
AC:
5868
AN:
68018
Other (OTH)
AF:
0.135
AC:
285
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
830
1660
2490
3320
4150
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
208
416
624
832
1040
<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:
0.130
Hom.:
412
Bravo
AF:
0.145
Asia WGS
AF:
0.0540
AC:
187
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Jul 23, 2019
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Atrial fibrillation, familial, 6 Benign:1
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Cardiac arrhythmia Benign:1
Aug 18, 2011
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.9
DANN
Benign
0.75
PhyloP100
-0.52
PromoterAI
-0.021
Neutral
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs5064; hg19: chr1-11907603; COSMIC: COSV56739762; COSMIC: COSV56739762; API