chr5-137753551-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006805.4(HNRNPA0):āc.516A>Gā(p.Lys172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000805 in 1,613,016 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0038 ( 6 hom., cov: 33)
Exomes š: 0.00049 ( 6 hom. )
Consequence
HNRNPA0
NM_006805.4 synonymous
NM_006805.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.81
Genes affected
HNRNPA0 (HGNC:5030): (heterogeneous nuclear ribonucleoprotein A0) This gene belongs to the A/B subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two repeats of quasi-RRM domains that bind RNAs, followed by a glycine-rich C-terminus. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 5-137753551-T-C is Benign according to our data. Variant chr5-137753551-T-C is described in ClinVar as [Benign]. Clinvar id is 709391.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.81 with no splicing effect.
BS2
High AC in GnomAd4 at 582 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNRNPA0 | NM_006805.4 | c.516A>G | p.Lys172= | synonymous_variant | 1/1 | ENST00000314940.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNRNPA0 | ENST00000314940.7 | c.516A>G | p.Lys172= | synonymous_variant | 1/1 | NM_006805.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00382 AC: 582AN: 152164Hom.: 6 Cov.: 33
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GnomAD3 exomes AF: 0.00105 AC: 263AN: 250070Hom.: 3 AF XY: 0.000834 AC XY: 113AN XY: 135542
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GnomAD4 exome AF: 0.000491 AC: 717AN: 1460734Hom.: 6 Cov.: 32 AF XY: 0.000449 AC XY: 326AN XY: 726450
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GnomAD4 genome AF: 0.00382 AC: 582AN: 152282Hom.: 6 Cov.: 33 AF XY: 0.00352 AC XY: 262AN XY: 74470
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 12, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at