2-88084408-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_198274.4(SMYD1):c.230C>T(p.Thr77Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,609,152 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_198274.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMYD1 | ENST00000419482.7 | c.230C>T | p.Thr77Ile | missense_variant | Exon 2 of 10 | 1 | NM_198274.4 | ENSP00000393453.2 | ||
SMYD1 | ENST00000444564.2 | c.230C>T | p.Thr77Ile | missense_variant | Exon 2 of 9 | 5 | ENSP00000407888.2 | |||
SMYD1 | ENST00000438570.1 | c.230C>T | p.Thr77Ile | missense_variant | Exon 2 of 3 | 2 | ENSP00000387482.1 | |||
SMYD1 | ENST00000468008.1 | n.260C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251480Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135910
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1456948Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 724250
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.230C>T (p.T77I) alteration is located in exon 2 (coding exon 2) of the SMYD1 gene. This alteration results from a C to T substitution at nucleotide position 230, causing the threonine (T) at amino acid position 77 to be replaced by an isoleucine (I). 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