chr1-153685711-A-T
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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
NM_000906.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0280
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 |
---|---|---|---|---|---|---|---|---|
NPR1 | NM_000906.4 | c.1606-95A>T | intron_variant | ENST00000368680.4 | NP_000897.3 | |||
NPR1 | XM_005245218.3 | c.1606-95A>T | intron_variant | XP_005245275.1 | ||||
NPR1 | XM_017001374.3 | c.1606-95A>T | intron_variant | XP_016856863.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPR1 | ENST00000368680.4 | c.1606-95A>T | intron_variant | 1 | NM_000906.4 | ENSP00000357669 | P1 |
Frequencies
GnomAD3 genomes AF: 0.111 AC: 16794AN: 151950Hom.: 1270 Cov.: 31
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GnomAD4 exome AF: 0.0765 AC: 58969AN: 770922Hom.: 2933 AF XY: 0.0774 AC XY: 31470AN XY: 406610
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GnomAD4 genome AF: 0.111 AC: 16834AN: 152066Hom.: 1284 Cov.: 31 AF XY: 0.109 AC XY: 8103AN XY: 74350
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at