chr6-45003751-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003599.4(SUPT3H):c.406A>T(p.Ile136Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,672 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 (★).
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.406A>T | p.Ile136Phe | missense_variant | Exon 6 of 11 | ENST00000371459.6 | NP_003590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUPT3H | ENST00000371459.6 | c.406A>T | p.Ile136Phe | missense_variant | Exon 6 of 11 | 1 | NM_003599.4 | ENSP00000360514.1 | ||
SUPT3H | ENST00000371460.5 | c.439A>T | p.Ile147Phe | missense_variant | Exon 8 of 13 | 1 | ENSP00000360515.1 | |||
SUPT3H | ENST00000637763.2 | c.220A>T | p.Ile74Phe | missense_variant | Exon 4 of 9 | 3 | ENSP00000490652.2 | |||
SUPT3H | ENST00000475057.5 | n.406A>T | non_coding_transcript_exon_variant | Exon 6 of 12 | 2 | ENSP00000436411.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250956Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135660
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461498Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727054
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.439A>T (p.I147F) alteration is located in exon 8 (coding exon 6) of the SUPT3H gene. This alteration results from a A to T substitution at nucleotide position 439, causing the isoleucine (I) at amino acid position 147 to be replaced by a phenylalanine (F). 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