2-73214283-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006062.3(SMYD5):c.17G>A(p.Cys6Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006062.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMYD5 | NM_006062.3 | c.17G>A | p.Cys6Tyr | missense_variant | 1/13 | ENST00000389501.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMYD5 | ENST00000389501.9 | c.17G>A | p.Cys6Tyr | missense_variant | 1/13 | 1 | NM_006062.3 | P1 | |
SMYD5 | ENST00000629411.2 | c.17G>A | p.Cys6Tyr | missense_variant | 1/3 | 5 | |||
SMYD5 | ENST00000413491.5 | c.17G>A | p.Cys6Tyr | missense_variant, NMD_transcript_variant | 1/5 | 4 | |||
SMYD5 | ENST00000258100.8 | c.17G>A | p.Cys6Tyr | missense_variant, NMD_transcript_variant | 1/8 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461620Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727128
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.17G>A (p.C6Y) alteration is located in exon 1 (coding exon 1) of the SMYD5 gene. This alteration results from a G to A substitution at nucleotide position 17, causing the cysteine (C) at amino acid position 6 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.