12-50081292-A-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001095.4(ASIC1):āc.1410A>Cā(p.Lys470Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,610,502 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001095.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASIC1 | NM_001095.4 | c.1410A>C | p.Lys470Asn | missense_variant | 11/12 | ENST00000447966.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASIC1 | ENST00000447966.7 | c.1410A>C | p.Lys470Asn | missense_variant | 11/12 | 1 | NM_001095.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000784 AC: 19AN: 242444Hom.: 0 AF XY: 0.0000837 AC XY: 11AN XY: 131436
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1458198Hom.: 0 Cov.: 34 AF XY: 0.0000262 AC XY: 19AN XY: 725034
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.1548A>C (p.K516N) alteration is located in exon 11 (coding exon 10) of the ASIC1 gene. This alteration results from a A to C substitution at nucleotide position 1548, causing the lysine (K) at amino acid position 516 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at