2-171965411-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003642.4(HAT1):c.383C>T(p.Ser128Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,610,326 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003642.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HAT1 | NM_003642.4 | c.383C>T | p.Ser128Phe | missense_variant | Exon 5 of 11 | ENST00000264108.5 | NP_003633.2 | |
HAT1 | XM_006712808.4 | c.365C>T | p.Ser122Phe | missense_variant | Exon 6 of 12 | XP_006712871.1 | ||
HAT1 | NR_027862.2 | n.347C>T | non_coding_transcript_exon_variant | Exon 4 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458208Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 725610
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.383C>T (p.S128F) alteration is located in exon 5 (coding exon 5) of the HAT1 gene. This alteration results from a C to T substitution at nucleotide position 383, causing the serine (S) at amino acid position 128 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