rs2075800
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005527.4(HSPA1L):c.1804G>A(p.Glu602Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,526,028 control chromosomes in the GnomAD database, including 78,497 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005527.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA1L | NM_005527.4 | c.1804G>A | p.Glu602Lys | missense_variant | 2/2 | ENST00000375654.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA1L | ENST00000375654.5 | c.1804G>A | p.Glu602Lys | missense_variant | 2/2 | 1 | NM_005527.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.256 AC: 38959AN: 151994Hom.: 6360 Cov.: 32
GnomAD3 exomes AF: 0.322 AC: 57626AN: 179186Hom.: 10244 AF XY: 0.329 AC XY: 31032AN XY: 94420
GnomAD4 exome AF: 0.317 AC: 436075AN: 1373916Hom.: 72131 Cov.: 36 AF XY: 0.320 AC XY: 216215AN XY: 675512
GnomAD4 genome AF: 0.256 AC: 38974AN: 152112Hom.: 6366 Cov.: 32 AF XY: 0.258 AC XY: 19212AN XY: 74336
ClinVar
Submissions by phenotype
HSPA1L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | 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