17-2056344-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001098202.1(HIC1):āc.35C>Gā(p.Ser12Trp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,613,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001098202.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152208Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249324Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135362
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1460842Hom.: 0 Cov.: 30 AF XY: 0.0000537 AC XY: 39AN XY: 726784
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152208Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2022 | The c.35C>G (p.S12W) alteration is located in exon 1 (coding exon 1) of the HIC1 gene. This alteration results from a C to G substitution at nucleotide position 35, causing the serine (S) at amino acid position 12 to be replaced by a tryptophan (W). 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