16-56939282-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_014685.4(HERPUD1):c.477C>G(p.Phe159Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000681 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014685.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HERPUD1 | NM_014685.4 | c.477C>G | p.Phe159Leu | missense_variant | Exon 5 of 8 | ENST00000439977.7 | NP_055500.1 | |
HERPUD1 | NM_001010989.3 | c.474C>G | p.Phe158Leu | missense_variant | Exon 5 of 8 | NP_001010989.1 | ||
HERPUD1 | NM_001272103.2 | c.477C>G | p.Phe159Leu | missense_variant | Exon 5 of 8 | NP_001259032.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152256Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727232
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.477C>G (p.F159L) alteration is located in exon 5 (coding exon 5) of the HERPUD1 gene. This alteration results from a C to G substitution at nucleotide position 477, causing the phenylalanine (F) at amino acid position 159 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