14-64541998-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_021979.4(HSPA2):c.1149C>T(p.Leu383=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000361 in 1,613,530 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00020 ( 3 hom. )
Consequence
HSPA2
NM_021979.4 synonymous
NM_021979.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.363
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 -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 14-64541998-C-T is Benign according to our data. Variant chr14-64541998-C-T is described in ClinVar as [Benign]. Clinvar id is 790145.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.363 with no splicing effect.
BS2
High AC in GnomAd4 at 296 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPA2 | NM_021979.4 | c.1149C>T | p.Leu383= | synonymous_variant | 1/1 | ENST00000247207.7 | NP_068814.2 | |
HSPA2 | NM_001387931.1 | c.1149C>T | p.Leu383= | synonymous_variant | 2/2 | NP_001374860.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSPA2 | ENST00000247207.7 | c.1149C>T | p.Leu383= | synonymous_variant | 1/1 | NM_021979.4 | ENSP00000247207 | P1 | ||
HSPA2 | ENST00000394709.2 | c.1149C>T | p.Leu383= | synonymous_variant | 2/2 | 1 | ENSP00000378199 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00195 AC: 296AN: 152132Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.000426 AC: 107AN: 250924Hom.: 1 AF XY: 0.000309 AC XY: 42AN XY: 135822
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GnomAD4 exome AF: 0.000196 AC: 286AN: 1461280Hom.: 3 Cov.: 86 AF XY: 0.000162 AC XY: 118AN XY: 726962
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GnomAD4 genome AF: 0.00194 AC: 296AN: 152250Hom.: 1 Cov.: 31 AF XY: 0.00191 AC XY: 142AN XY: 74442
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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 | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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