rs1557113917
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_005334.3(HCFC1):c.3829G>T(p.Ala1277Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 1,097,403 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1277T) has been classified as Uncertain significance.
Frequency
Consequence
NM_005334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.3829G>T | p.Ala1277Ser | missense_variant | 17/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.3829G>T | p.Ala1277Ser | missense_variant | 17/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.3829G>T | p.Ala1277Ser | missense_variant | 17/26 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097403Hom.: 0 Cov.: 34 AF XY: 0.0000165 AC XY: 6AN XY: 362935
GnomAD4 genome ? Cov.: 25
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at