12-50077326-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_001095.4(ASIC1):c.672C>T(p.Ile224=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0053 in 1,614,170 control chromosomes in the GnomAD database, including 407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.028 ( 208 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 199 hom. )
Consequence
ASIC1
NM_001095.4 synonymous
NM_001095.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.130
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BP6
?
Variant 12-50077326-C-T is Benign according to our data. Variant chr12-50077326-C-T is described in ClinVar as [Benign]. Clinvar id is 783660.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=-0.13 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASIC1 | NM_001095.4 | c.672C>T | p.Ile224= | synonymous_variant | 4/12 | ENST00000447966.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASIC1 | ENST00000447966.7 | c.672C>T | p.Ile224= | synonymous_variant | 4/12 | 1 | NM_001095.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0280 AC: 4262AN: 152184Hom.: 207 Cov.: 32
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GnomAD3 exomes AF: 0.00736 AC: 1850AN: 251312Hom.: 88 AF XY: 0.00488 AC XY: 663AN XY: 135874
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GnomAD4 exome AF: 0.00293 AC: 4281AN: 1461868Hom.: 199 Cov.: 31 AF XY: 0.00247 AC XY: 1798AN XY: 727238
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GnomAD4 genome ? AF: 0.0281 AC: 4280AN: 152302Hom.: 208 Cov.: 32 AF XY: 0.0274 AC XY: 2037AN XY: 74470
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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 | Jul 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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