17-2057693-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_006497.4(HIC1):c.1003G>C(p.Glu335Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,486,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006497.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIC1 | NM_006497.4 | c.1003G>C | p.Glu335Gln | missense_variant | 2/2 | ENST00000619757.5 | |
HIC1 | NM_001098202.1 | c.1060G>C | p.Glu354Gln | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIC1 | ENST00000619757.5 | c.1003G>C | p.Glu335Gln | missense_variant | 2/2 | 1 | NM_006497.4 | P4 | |
HIC1 | ENST00000399849.4 | c.1003G>C | p.Glu335Gln | missense_variant | 2/2 | 1 | P4 | ||
HIC1 | ENST00000322941.3 | c.1060G>C | p.Glu354Gln | missense_variant | 2/2 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151730Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000560 AC: 5AN: 89212Hom.: 0 AF XY: 0.0000781 AC XY: 4AN XY: 51214
GnomAD4 exome AF: 0.000121 AC: 162AN: 1334602Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 80AN XY: 659290
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151730Hom.: 0 Cov.: 34 AF XY: 0.0000540 AC XY: 4AN XY: 74118
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.1060G>C (p.E354Q) alteration is located in exon 2 (coding exon 2) of the HIC1 gene. This alteration results from a G to C substitution at nucleotide position 1060, causing the glutamic acid (E) at amino acid position 354 to be replaced by a glutamine (Q). 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