chr6-45014864-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003599.4(SUPT3H):āc.301A>Cā(p.Met101Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000187 in 1,589,544 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003599.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUPT3H | NM_003599.4 | c.301A>C | p.Met101Leu | missense_variant | Exon 5 of 11 | ENST00000371459.6 | NP_003590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUPT3H | ENST00000371459.6 | c.301A>C | p.Met101Leu | missense_variant | Exon 5 of 11 | 1 | NM_003599.4 | ENSP00000360514.1 | ||
SUPT3H | ENST00000371460.5 | c.334A>C | p.Met112Leu | missense_variant | Exon 7 of 13 | 1 | ENSP00000360515.1 | |||
SUPT3H | ENST00000637763.2 | c.115A>C | p.Met39Leu | missense_variant | Exon 3 of 9 | 3 | ENSP00000490652.2 | |||
SUPT3H | ENST00000475057.5 | n.301A>C | non_coding_transcript_exon_variant | Exon 5 of 12 | 2 | ENSP00000436411.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152120Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 14AN: 234488Hom.: 0 AF XY: 0.0000551 AC XY: 7AN XY: 126968
GnomAD4 exome AF: 0.000201 AC: 289AN: 1437424Hom.: 0 Cov.: 29 AF XY: 0.000179 AC XY: 128AN XY: 714350
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.334A>C (p.M112L) alteration is located in exon 7 (coding exon 5) of the SUPT3H gene. This alteration results from a A to C substitution at nucleotide position 334, causing the methionine (M) at amino acid position 112 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