11-123057829-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 8P and 4B. PVS1BS2
The NM_153201.4(HSPA8):c.1388-1G>A variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153201.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPA8 | NM_006597.6 | c.1846G>A | p.Gly616Ser | missense_variant | Exon 9 of 9 | ENST00000534624.6 | NP_006588.1 | |
HSPA8 | XM_011542798.2 | c.1846G>A | p.Gly616Ser | missense_variant | Exon 9 of 9 | XP_011541100.1 | ||
HSPA8 | NM_153201.4 | c.1388-1G>A | splice_acceptor_variant, intron_variant | Intron 7 of 7 | NP_694881.1 | |||
SNORD14E | NR_003125.2 | n.*248G>A | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251038Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135686
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461542Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727086
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1846G>A (p.G616S) alteration is located in exon 9 (coding exon 8) of the HSPA8 gene. This alteration results from a G to A substitution at nucleotide position 1846, causing the glycine (G) at amino acid position 616 to be replaced by a serine (S). 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