chr7-44966219-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033054.3(MYO1G):c.2011G>A(p.Val671Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000335 in 1,612,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000034 ( 0 hom. )
Consequence
MYO1G
NM_033054.3 missense
NM_033054.3 missense
Scores
2
15
2
Clinical Significance
Conservation
PhyloP100: 4.75
Genes affected
MYO1G (HGNC:13880): (myosin IG) MYO1G is a plasma membrane-associated class I myosin (see MIM 601478) that is abundant in T and B lymphocytes and mast cells (Pierce et al., 2001 [PubMed 11544309]; Patino-Lopez et al., 2010 [PubMed 20071333]).[supplied by OMIM, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1G | NM_033054.3 | c.2011G>A | p.Val671Met | missense_variant | 16/22 | ENST00000258787.12 | |
MYO1G | XR_007060129.1 | n.2065G>A | non_coding_transcript_exon_variant | 16/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1G | ENST00000258787.12 | c.2011G>A | p.Val671Met | missense_variant | 16/22 | 1 | NM_033054.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152096Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247638Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134406
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GnomAD4 exome AF: 0.0000336 AC: 49AN: 1460180Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 726372
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152096Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74264
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.2011G>A (p.V671M) alteration is located in exon 16 (coding exon 16) of the MYO1G gene. This alteration results from a G to A substitution at nucleotide position 2011, causing the valine (V) at amino acid position 671 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;.
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.
REVEL
Uncertain
Sift
Uncertain
D;.
Sift4G
Uncertain
D;.
Polyphen
D;.
Vest4
MutPred
Gain of disorder (P = 0.0778);Gain of disorder (P = 0.0778);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at