chr10-67925118-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015601.4(HERC4):c.2908G>A(p.Glu970Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,601,320 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_015601.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HERC4 | NM_015601.4 | c.2908G>A | p.Glu970Lys | missense_variant | Exon 24 of 25 | ENST00000373700.9 | NP_056416.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250790Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135588
GnomAD4 exome AF: 0.000139 AC: 201AN: 1449172Hom.: 0 Cov.: 27 AF XY: 0.000139 AC XY: 100AN XY: 721786
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2932G>A (p.E978K) alteration is located in exon 25 (coding exon 23) of the HERC4 gene. This alteration results from a G to A substitution at nucleotide position 2932, causing the glutamic acid (E) at amino acid position 978 to be replaced by a lysine (K). 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