chr14-64542508-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_021979.4(HSPA2):c.1659G>A(p.Lys553=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00355 in 1,613,384 control chromosomes in the GnomAD database, including 173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.019 ( 81 hom., cov: 31)
Exomes 𝑓: 0.0020 ( 92 hom. )
Consequence
HSPA2
NM_021979.4 synonymous
NM_021979.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.66
Genes affected
HSPA2 (HGNC:5235): (heat shock protein family A (Hsp70) member 2) Enables disordered domain specific binding activity; enzyme binding activity; and unfolded protein binding activity. Involved in negative regulation of inclusion body assembly and protein refolding. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant 14-64542508-G-A is Benign according to our data. Variant chr14-64542508-G-A is described in ClinVar as [Benign]. Clinvar id is 779688.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0633 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPA2 | NM_021979.4 | c.1659G>A | p.Lys553= | synonymous_variant | 1/1 | ENST00000247207.7 | NP_068814.2 | |
HSPA2 | NM_001387931.1 | c.1659G>A | p.Lys553= | synonymous_variant | 2/2 | NP_001374860.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSPA2 | ENST00000247207.7 | c.1659G>A | p.Lys553= | synonymous_variant | 1/1 | NM_021979.4 | ENSP00000247207 | P1 | ||
HSPA2 | ENST00000394709.2 | c.1659G>A | p.Lys553= | synonymous_variant | 2/2 | 1 | ENSP00000378199 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0187 AC: 2828AN: 151580Hom.: 81 Cov.: 31
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GnomAD3 exomes AF: 0.00519 AC: 1302AN: 250704Hom.: 44 AF XY: 0.00371 AC XY: 504AN XY: 135678
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GnomAD4 exome AF: 0.00198 AC: 2890AN: 1461686Hom.: 92 Cov.: 83 AF XY: 0.00169 AC XY: 1226AN XY: 727122
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GnomAD4 genome AF: 0.0187 AC: 2831AN: 151698Hom.: 81 Cov.: 31 AF XY: 0.0184 AC XY: 1362AN XY: 74080
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at