chr2-197487154-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_002156.5(HSPD1):c.1614G>C(p.Leu538=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,459,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L538L) has been classified as Likely benign.
Frequency
Consequence
NM_002156.5 synonymous
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 |
---|---|---|---|---|---|---|---|
HSPD1 | NM_002156.5 | c.1614G>C | p.Leu538= | synonymous_variant | 12/12 | ENST00000388968.8 | |
HSPD1 | NM_199440.2 | c.1614G>C | p.Leu538= | synonymous_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPD1 | ENST00000388968.8 | c.1614G>C | p.Leu538= | synonymous_variant | 12/12 | 1 | NM_002156.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248780Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135210
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459534Hom.: 0 Cov.: 29 AF XY: 0.00000826 AC XY: 6AN XY: 726196
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at