6-118907469-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014034.3(ASF1A):c.470C>T(p.Thr157Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000093 in 1,613,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014034.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASF1A | ENST00000229595.6 | c.470C>T | p.Thr157Ile | missense_variant | Exon 4 of 4 | 1 | NM_014034.3 | ENSP00000229595.5 | ||
MCM9 | ENST00000619706.5 | c.1150+4181G>A | intron_variant | Intron 8 of 13 | 5 | NM_017696.3 | ENSP00000480469.1 | |||
MCM9 | ENST00000316316.10 | c.1150+4181G>A | intron_variant | Intron 7 of 12 | 5 | ENSP00000314505.5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247766Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134426
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1460900Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726672
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.470C>T (p.T157I) alteration is located in exon 4 (coding exon 4) of the ASF1A gene. This alteration results from a C to T substitution at nucleotide position 470, causing the threonine (T) at amino acid position 157 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