1-1285631-C-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001130413.4(SCNN1D):c.525C>A(p.Pro175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000205 in 1,547,490 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
SCNN1D
NM_001130413.4 synonymous
NM_001130413.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.188
Genes affected
SCNN1D (HGNC:10601): (sodium channel epithelial 1 subunit delta) Predicted to enable ligand-gated sodium channel activity. Predicted to be involved in sodium ion transmembrane transport. Located in actin cytoskeleton and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
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Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
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Variant 1-1285631-C-A is Benign according to our data. Variant chr1-1285631-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2672317.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-1285631-C-A is described in Lovd as [Likely_benign].
BP7
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Synonymous conserved (PhyloP=0.188 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCNN1D | NM_001130413.4 | c.525C>A | p.Pro175= | synonymous_variant | 6/18 | ENST00000379116.10 | |
SCNN1D | NR_037668.3 | n.691-295C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1D | ENST00000379116.10 | c.525C>A | p.Pro175= | synonymous_variant | 6/18 | 5 | NM_001130413.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152236Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000245 AC: 37AN: 150832Hom.: 1 AF XY: 0.000262 AC XY: 21AN XY: 80216
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GnomAD4 exome AF: 0.000211 AC: 294AN: 1395254Hom.: 1 Cov.: 31 AF XY: 0.000212 AC XY: 146AN XY: 687972
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GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152236Hom.: 0 Cov.: 34 AF XY: 0.000188 AC XY: 14AN XY: 74368
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | SCNN1D: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at