16-23302732-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000336.3(SCNN1B):c.-9+295T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,884 control chromosomes in the GnomAD database, including 8,278 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.31 ( 8278 hom., cov: 31)
Consequence
SCNN1B
NM_000336.3 intron
NM_000336.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.17
Genes affected
SCNN1B (HGNC:10600): (sodium channel epithelial 1 subunit beta) Nonvoltage-gated, amiloride-sensitive, sodium channels control fluid and electrolyte transport across epithelia in many organs. These channels are heteromeric complexes consisting of 3 subunits: alpha, beta, and gamma. This gene encodes the beta subunit, and mutations in this gene have been associated with pseudohypoaldosteronism type 1 (PHA1), and Liddle syndrome. [provided by RefSeq, Apr 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 16-23302732-T-C is Benign according to our data. Variant chr16-23302732-T-C is described in ClinVar as [Benign]. Clinvar id is 1261922.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCNN1B | NM_000336.3 | c.-9+295T>C | intron_variant | ENST00000343070.7 | |||
SCNN1B | NM_001410900.1 | c.-9+295T>C | intron_variant | ||||
SCNN1B | XM_011545913.3 | c.-1+295T>C | intron_variant | ||||
SCNN1B | XM_017023525.2 | c.49+18928T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1B | ENST00000343070.7 | c.-9+295T>C | intron_variant | 1 | NM_000336.3 | P1 | |||
SCNN1B | ENST00000569789.1 | n.178+18928T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.307 AC: 46536AN: 151766Hom.: 8245 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.307 AC: 46608AN: 151884Hom.: 8278 Cov.: 31 AF XY: 0.306 AC XY: 22709AN XY: 74230
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 14, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at