rs1859999
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003802.3(MYH13):c.2692-1234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,846 control chromosomes in the GnomAD database, including 27,077 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.59 ( 27077 hom., cov: 31)
Consequence
MYH13
NM_003802.3 intron
NM_003802.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.549
Genes affected
MYH13 (HGNC:7571): (myosin heavy chain 13) Predicted to enable microfilament motor activity. Predicted to be involved in muscle contraction. Predicted to act upstream of or within cellular response to starvation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH13 | NM_003802.3 | c.2692-1234T>C | intron_variant | ENST00000252172.9 | |||
LOC107985004 | XR_007065617.1 | n.681+4986A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH13 | ENST00000252172.9 | c.2692-1234T>C | intron_variant | 1 | NM_003802.3 | P1 | |||
MYH13 | ENST00000621918.1 | c.2692-1234T>C | intron_variant | 1 | P1 | ||||
ENST00000577743.1 | n.246+531A>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
MYH13 | ENST00000418404.8 | c.2692-1234T>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.593 AC: 89937AN: 151728Hom.: 27069 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.593 AC: 89987AN: 151846Hom.: 27077 Cov.: 31 AF XY: 0.587 AC XY: 43561AN XY: 74180
GnomAD4 genome
?
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89987
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151846
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31
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43561
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74180
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1523
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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