chr9-125238999-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_005347.5(HSPA5):c.938A>G(p.Tyr313Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,613,892 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts 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. Y313H) has been classified as Uncertain significance.
Frequency
Consequence
NM_005347.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA5 | NM_005347.5 | c.938A>G | p.Tyr313Cys | missense_variant | 5/8 | ENST00000324460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA5 | ENST00000324460.7 | c.938A>G | p.Tyr313Cys | missense_variant | 5/8 | 1 | NM_005347.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251106Hom.: 1 AF XY: 0.000324 AC XY: 44AN XY: 135808
GnomAD4 exome AF: 0.000108 AC: 158AN: 1461572Hom.: 2 Cov.: 32 AF XY: 0.000157 AC XY: 114AN XY: 727104
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | The c.938A>G (p.Y313C) alteration is located in exon 5 (coding exon 5) of the HSPA5 gene. This alteration results from a A to G substitution at nucleotide position 938, causing the tyrosine (Y) at amino acid position 313 to be replaced by a cysteine (C). 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