12-57028802-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005379.4(MYO1A):c.3085C>T(p.Arg1029Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005379.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.3085C>T | p.Arg1029Cys | missense_variant | 28/28 | ENST00000300119.8 | NP_005370.1 | |
MYO1A | NM_001256041.2 | c.3085C>T | p.Arg1029Cys | missense_variant | 29/29 | NP_001242970.1 | ||
MYO1A | XM_047428876.1 | c.3085C>T | p.Arg1029Cys | missense_variant | 29/29 | XP_047284832.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.3085C>T | p.Arg1029Cys | missense_variant | 28/28 | 1 | NM_005379.4 | ENSP00000300119 | P1 | |
MYO1A | ENST00000442789.6 | c.3085C>T | p.Arg1029Cys | missense_variant | 29/29 | 1 | ENSP00000393392 | P1 | ||
TAC3 | ENST00000415231.1 | c.-140C>T | 5_prime_UTR_variant | 1/7 | 5 | ENSP00000402995 | P1 | |||
MYO1A | ENST00000554234.5 | c.*530C>T | 3_prime_UTR_variant, NMD_transcript_variant | 24/24 | 5 | ENSP00000451033 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151794Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249582Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135072
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461640Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727146
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151794Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74092
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.3085C>T (p.R1029C) alteration is located in exon 28 (coding exon 27) of the MYO1A gene. This alteration results from a C to T substitution at nucleotide position 3085, causing the arginine (R) at amino acid position 1029 to be replaced by a cysteine (C). 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