2-88087990-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198274.4(SMYD1):c.443G>T(p.Arg148Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,614,068 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_198274.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMYD1 | NM_198274.4 | c.443G>T | p.Arg148Leu | missense_variant | 3/10 | ENST00000419482.7 | NP_938015.1 | |
SMYD1 | NM_001330364.2 | c.443G>T | p.Arg148Leu | missense_variant | 3/9 | NP_001317293.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMYD1 | ENST00000419482.7 | c.443G>T | p.Arg148Leu | missense_variant | 3/10 | 1 | NM_198274.4 | ENSP00000393453.2 | ||
SMYD1 | ENST00000444564.2 | c.443G>T | p.Arg148Leu | missense_variant | 3/9 | 5 | ENSP00000407888.2 | |||
SMYD1 | ENST00000438570.1 | c.294+3518G>T | intron_variant | 2 | ENSP00000387482.1 | |||||
SMYD1 | ENST00000468008.1 | n.473G>T | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251338Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135840
GnomAD4 exome AF: 0.000148 AC: 217AN: 1461878Hom.: 0 Cov.: 33 AF XY: 0.000147 AC XY: 107AN XY: 727236
GnomAD4 genome AF: 0.000243 AC: 37AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 24, 2023 | The c.443G>T (p.R148L) alteration is located in exon 3 (coding exon 3) of the SMYD1 gene. This alteration results from a G to T substitution at nucleotide position 443, causing the arginine (R) at amino acid position 148 to be replaced by a leucine (L). 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