17-10444671-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_017533.2(MYH4):c.5600G>A(p.Arg1867Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017533.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH4 | NM_017533.2 | c.5600G>A | p.Arg1867Lys | missense_variant | Exon 39 of 40 | ENST00000255381.2 | NP_060003.2 | |
MYH4 | XM_017024676.2 | c.5600G>A | p.Arg1867Lys | missense_variant | Exon 37 of 38 | XP_016880165.1 | ||
MYHAS | NR_125367.1 | n.167+38433C>T | intron_variant | Intron 2 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH4 | ENST00000255381.2 | c.5600G>A | p.Arg1867Lys | missense_variant | Exon 39 of 40 | 1 | NM_017533.2 | ENSP00000255381.2 | ||
ENSG00000272736 | ENST00000399342.6 | n.206+38394C>T | intron_variant | Intron 2 of 3 | 3 | |||||
ENSG00000272736 | ENST00000581304.1 | n.143+38433C>T | intron_variant | Intron 2 of 3 | 3 | |||||
MYHAS | ENST00000587182.2 | n.155+38433C>T | intron_variant | Intron 2 of 10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152000Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727222
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5600G>A (p.R1867K) alteration is located in exon 39 (coding exon 37) of the MYH4 gene. This alteration results from a G to A substitution at nucleotide position 5600, causing the arginine (R) at amino acid position 1867 to be replaced by a lysine (K). 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