1-32889192-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_002143.3(HPCA):c.294G>A(p.Glu98=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
HPCA
NM_002143.3 synonymous
NM_002143.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.42
Genes affected
HPCA (HGNC:5144): (hippocalcin) The protein encoded by this gene is a member of neuron-specific calcium-binding proteins family found in the retina and brain. This protein is associated with the plasma membrane. It has similarities to proteins located in the photoreceptor cells that regulate photosignal transduction in a calcium-sensitive manner. This protein displays recoverin activity and a calcium-dependent inhibition of rhodopsin kinase. It is identical to the rat and mouse hippocalcin proteins and thought to play an important role in neurons of the central nervous system in a number of species. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 1-32889192-G-A is Benign according to our data. Variant chr1-32889192-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2914582.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.42 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HPCA | NM_002143.3 | c.294G>A | p.Glu98= | synonymous_variant | 2/4 | ENST00000373467.4 | NP_002134.2 | |
HPCA | XM_005270792.4 | c.294G>A | p.Glu98= | synonymous_variant | 2/4 | XP_005270849.1 | ||
HPCA | XM_017001118.3 | c.294G>A | p.Glu98= | synonymous_variant | 2/4 | XP_016856607.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HPCA | ENST00000373467.4 | c.294G>A | p.Glu98= | synonymous_variant | 2/4 | 1 | NM_002143.3 | ENSP00000362566 | P1 | |
HPCA | ENST00000480118.5 | n.353G>A | non_coding_transcript_exon_variant | 2/3 | 5 | |||||
HPCA | ENST00000459874.5 | n.54+2677G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
HPCA | ENST00000470166.5 | n.126+3073G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251418Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135890
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GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727248
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152382Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74524
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | - - |
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