chr2-191390422-T-G
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_Strong
The NM_001130158.3(MYO1B):c.1912T>G(p.Tyr638Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 152,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130158.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1B | NM_001130158.3 | c.1912T>G | p.Tyr638Asp | missense_variant | 18/31 | ENST00000392318.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1B | ENST00000392318.8 | c.1912T>G | p.Tyr638Asp | missense_variant | 18/31 | 1 | NM_001130158.3 | P1 | |
MYO1B | ENST00000304164.8 | c.1912T>G | p.Tyr638Asp | missense_variant | 18/31 | 1 | P1 | ||
MYO1B | ENST00000339514.8 | c.1912T>G | p.Tyr638Asp | missense_variant | 18/29 | 1 | |||
MYO1B | ENST00000392316.5 | c.1912T>G | p.Tyr638Asp | missense_variant | 17/29 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251428Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135892
GnomAD4 exome Cov.: 31
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.1912T>G (p.Y638D) alteration is located in exon 18 (coding exon 17) of the MYO1B gene. This alteration results from a T to G substitution at nucleotide position 1912, causing the tyrosine (Y) at amino acid position 638 to be replaced by an aspartic acid (D). 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