10-14867739-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_016299.4(HSPA14):c.1210G>C(p.Val404Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,024 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_016299.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA14 | NM_016299.4 | c.1210G>C | p.Val404Leu | missense_variant | 12/14 | ENST00000378372.8 | |
LOC124902382 | XR_007062064.1 | n.370C>G | non_coding_transcript_exon_variant | 2/3 | |||
LOC124902382 | XR_007062065.1 | n.370C>G | non_coding_transcript_exon_variant | 2/3 | |||
LOC124902382 | XR_007062066.1 | n.370C>G | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA14 | ENST00000378372.8 | c.1210G>C | p.Val404Leu | missense_variant | 12/14 | 1 | NM_016299.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 249964Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135096
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460768Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726692
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2022 | The c.1210G>C (p.V404L) alteration is located in exon 12 (coding exon 12) of the HSPA14 gene. This alteration results from a G to C substitution at nucleotide position 1210, causing the valine (V) at amino acid position 404 to be replaced by a leucine (L). 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