6-31810752-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_005527.4(HSPA1L):c.1221G>A(p.Thr407Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 1,613,840 control chromosomes in the GnomAD database, including 7,793 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_005527.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPA1L | NM_005527.4 | c.1221G>A | p.Thr407Thr | synonymous_variant | Exon 2 of 2 | ENST00000375654.5 | NP_005518.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.126 AC: 19142AN: 151848Hom.: 1592 Cov.: 32
GnomAD3 exomes AF: 0.103 AC: 25959AN: 251410Hom.: 1898 AF XY: 0.0982 AC XY: 13342AN XY: 135884
GnomAD4 exome AF: 0.0800 AC: 116982AN: 1461874Hom.: 6194 Cov.: 37 AF XY: 0.0798 AC XY: 58070AN XY: 727240
GnomAD4 genome AF: 0.126 AC: 19164AN: 151966Hom.: 1599 Cov.: 32 AF XY: 0.125 AC XY: 9286AN XY: 74254
ClinVar
Submissions by phenotype
HSPA1L-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at