7-44965714-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_033054.3(MYO1G):c.2304C>T(p.Tyr768=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,612,832 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00013 ( 2 hom. )
Consequence
MYO1G
NM_033054.3 synonymous
NM_033054.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.675
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 Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 7-44965714-G-A is Benign according to our data. Variant chr7-44965714-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3164045.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.675 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1G | NM_033054.3 | c.2304C>T | p.Tyr768= | synonymous_variant | 17/22 | ENST00000258787.12 | |
MYO1G | XR_007060129.1 | n.2358C>T | non_coding_transcript_exon_variant | 17/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1G | ENST00000258787.12 | c.2304C>T | p.Tyr768= | synonymous_variant | 17/22 | 1 | NM_033054.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152204Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000213 AC: 53AN: 248798Hom.: 0 AF XY: 0.000244 AC XY: 33AN XY: 135030
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GnomAD4 exome AF: 0.000126 AC: 184AN: 1460510Hom.: 2 Cov.: 32 AF XY: 0.000154 AC XY: 112AN XY: 726510
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GnomAD4 genome AF: 0.000243 AC: 37AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74494
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at