rs4713489
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005527.4(HSPA1L):c.-291C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0325 in 256,020 control chromosomes in the GnomAD database, including 222 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.042 ( 181 hom., cov: 30)
Exomes 𝑓: 0.020 ( 41 hom. )
Consequence
HSPA1L
NM_005527.4 5_prime_UTR
NM_005527.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.06
Genes affected
HSPA1L (HGNC:5234): (heat shock protein family A (Hsp70) member 1 like) This gene encodes a 70kDa heat shock protein. In conjunction with other heat shock proteins, this protein stabilizes existing proteins against aggregation and mediates the folding of newly translated proteins in the cytosol and in organelles. The gene is located in the major histocompatibility complex class III region, in a cluster with two closely related genes which also encode isoforms of the 70kDa heat shock protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA1L | NM_005527.4 | c.-291C>T | 5_prime_UTR_variant | 1/2 | ENST00000375654.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA1L | ENST00000375654.5 | c.-291C>T | 5_prime_UTR_variant | 1/2 | 1 | NM_005527.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0415 AC: 6257AN: 150632Hom.: 181 Cov.: 30
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GnomAD4 exome AF: 0.0197 AC: 2070AN: 105278Hom.: 41 AF XY: 0.0207 AC XY: 1065AN XY: 51376
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GnomAD4 genome ? AF: 0.0415 AC: 6257AN: 150742Hom.: 181 Cov.: 30 AF XY: 0.0414 AC XY: 3043AN XY: 73574
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at