chr1-153685711-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000906.4(NPR1):​c.1606-95A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 922,988 control chromosomes in the GnomAD database, including 4,217 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 0.11 ( 1284 hom., cov: 31)
Exomes 𝑓: 0.076 ( 2933 hom. )

Consequence

NPR1
NM_000906.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0280
Variant links:
Genes affected
NPR1 (HGNC:7943): (natriuretic peptide receptor 1) Guanylyl cyclases, catalyzing the production of cGMP from GTP, are classified as soluble and membrane forms (Garbers and Lowe, 1994 [PubMed 7982997]). The membrane guanylyl cyclases, often termed guanylyl cyclases A through F, form a family of cell-surface receptors with a similar topographic structure: an extracellular ligand-binding domain, a single membrane-spanning domain, and an intracellular region that contains a protein kinase-like domain and a cyclase catalytic domain. GC-A and GC-B function as receptors for natriuretic peptides; they are also referred to as atrial natriuretic peptide receptor A (NPR1) and type B (NPR2; MIM 108961). Also see NPR3 (MIM 108962), which encodes a protein with only the ligand-binding transmembrane and 37-amino acid cytoplasmic domains. NPR1 is a membrane-bound guanylate cyclase that serves as the receptor for both atrial and brain natriuretic peptides (ANP (MIM 108780) and BNP (MIM 600295), respectively).[supplied by OMIM, May 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NPR1NM_000906.4 linkuse as main transcriptc.1606-95A>T intron_variant ENST00000368680.4 NP_000897.3
NPR1XM_005245218.3 linkuse as main transcriptc.1606-95A>T intron_variant XP_005245275.1
NPR1XM_017001374.3 linkuse as main transcriptc.1606-95A>T intron_variant XP_016856863.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NPR1ENST00000368680.4 linkuse as main transcriptc.1606-95A>T intron_variant 1 NM_000906.4 ENSP00000357669 P1

Frequencies

GnomAD3 genomes
AF:
0.111
AC:
16794
AN:
151950
Hom.:
1270
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.216
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.0796
Gnomad ASJ
AF:
0.120
Gnomad EAS
AF:
0.00115
Gnomad SAS
AF:
0.0919
Gnomad FIN
AF:
0.0633
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.0705
Gnomad OTH
AF:
0.115
GnomAD4 exome
AF:
0.0765
AC:
58969
AN:
770922
Hom.:
2933
AF XY:
0.0774
AC XY:
31470
AN XY:
406610
show subpopulations
Gnomad4 AFR exome
AF:
0.231
Gnomad4 AMR exome
AF:
0.0590
Gnomad4 ASJ exome
AF:
0.122
Gnomad4 EAS exome
AF:
0.000165
Gnomad4 SAS exome
AF:
0.0972
Gnomad4 FIN exome
AF:
0.0606
Gnomad4 NFE exome
AF:
0.0724
Gnomad4 OTH exome
AF:
0.0893
GnomAD4 genome
AF:
0.111
AC:
16834
AN:
152066
Hom.:
1284
Cov.:
31
AF XY:
0.109
AC XY:
8103
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.217
Gnomad4 AMR
AF:
0.0794
Gnomad4 ASJ
AF:
0.120
Gnomad4 EAS
AF:
0.00116
Gnomad4 SAS
AF:
0.0918
Gnomad4 FIN
AF:
0.0633
Gnomad4 NFE
AF:
0.0705
Gnomad4 OTH
AF:
0.115
Alfa
AF:
0.0935
Hom.:
118
Bravo
AF:
0.117
Asia WGS
AF:
0.0530
AC:
185
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.2
DANN
Benign
0.65

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3891075; hg19: chr1-153658187; API