12-50080489-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001095.4(ASIC1):c.1206-9C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00376 in 1,613,646 control chromosomes in the GnomAD database, including 206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 109 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 97 hom. )
Consequence
ASIC1
NM_001095.4 splice_polypyrimidine_tract, intron
NM_001095.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0005725
2
Clinical Significance
Conservation
PhyloP100: 0.934
Genes affected
ASIC1 (HGNC:100): (acid sensing ion channel subunit 1) This gene encodes a member of the acid-sensing ion channel (ASIC) family of proteins, which are part of the degenerin/epithelial sodium channel (DEG/ENaC) superfamily. Members of the ASIC family are sensitive to amiloride and function in neurotransmission. The encoded proteins function in learning, pain transduction, touch sensation, and development of memory and fear. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2012]
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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=-0.51).
BP6
?
Variant 12-50080489-C-T is Benign according to our data. Variant chr12-50080489-C-T is described in ClinVar as [Benign]. Clinvar id is 784239.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASIC1 | NM_001095.4 | c.1206-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000447966.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASIC1 | ENST00000447966.7 | c.1206-9C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001095.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0200 AC: 3038AN: 152142Hom.: 109 Cov.: 33
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GnomAD3 exomes AF: 0.00504 AC: 1265AN: 251194Hom.: 41 AF XY: 0.00330 AC XY: 448AN XY: 135768
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GnomAD4 exome AF: 0.00207 AC: 3020AN: 1461386Hom.: 97 Cov.: 31 AF XY: 0.00173 AC XY: 1256AN XY: 727014
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GnomAD4 genome ? AF: 0.0200 AC: 3052AN: 152260Hom.: 109 Cov.: 33 AF XY: 0.0198 AC XY: 1471AN XY: 74450
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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 | Invitae | Apr 24, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at