13-31137500-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006644.4(HSPH1):c.2395G>A(p.Val799Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006644.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPH1 | NM_006644.4 | c.2395G>A | p.Val799Ile | missense_variant | 18/18 | ENST00000320027.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPH1 | ENST00000320027.10 | c.2395G>A | p.Val799Ile | missense_variant | 18/18 | 1 | NM_006644.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250806Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135572
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461168Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 726890
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.2395G>A (p.V799I) alteration is located in exon 18 (coding exon 18) of the HSPH1 gene. This alteration results from a G to A substitution at nucleotide position 2395, causing the valine (V) at amino acid position 799 to be replaced by an isoleucine (I). 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