chr10-116674831-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_025015.3(HSPA12A):c.1978A>G(p.Ile660Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,308 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I660T) has been classified as Uncertain significance.
Frequency
Consequence
NM_025015.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA12A | NM_025015.3 | c.1978A>G | p.Ile660Val | missense_variant | 12/12 | ENST00000369209.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA12A | ENST00000369209.8 | c.1978A>G | p.Ile660Val | missense_variant | 12/12 | 1 | NM_025015.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249040Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135232
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461234Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 726922
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1978A>G (p.I660V) alteration is located in exon 12 (coding exon 12) of the HSPA12A gene. This alteration results from a A to G substitution at nucleotide position 1978, causing the isoleucine (I) at amino acid position 660 to be replaced by a valine (V). 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