rs508543
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016257.4(HPCAL4):c.-9+2795T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,086 control chromosomes in the GnomAD database, including 10,136 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 0.34 ( 10136 hom., cov: 32)
Consequence
HPCAL4
NM_016257.4 intron
NM_016257.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.442
Genes affected
HPCAL4 (HGNC:18212): (hippocalcin like 4) The protein encoded by this gene is highly similar to human hippocalcin protein and hippocalcin like-1 protein. It also has similarity to rat neural visinin-like Ca2+-binding protein-type 1 and 2 proteins. This encoded protein may be involved in the calcium-dependent regulation of rhodopsin phosphorylation. The transcript of this gene has multiple polyadenylation sites. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPCAL4 | NM_016257.4 | c.-9+2795T>C | intron_variant | ENST00000372844.8 | |||
HPCAL4 | NM_001282396.2 | c.-9+2554T>C | intron_variant | ||||
HPCAL4 | NM_001282397.2 | c.-9+2795T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPCAL4 | ENST00000372844.8 | c.-9+2795T>C | intron_variant | 1 | NM_016257.4 | P1 | |||
HPCAL4 | ENST00000612703.3 | c.-9+2795T>C | intron_variant | 2 | |||||
HPCAL4 | ENST00000617690.2 | c.-9+2554T>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.341 AC: 51798AN: 151968Hom.: 10116 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.341 AC: 51837AN: 152086Hom.: 10136 Cov.: 32 AF XY: 0.350 AC XY: 26036AN XY: 74364
GnomAD4 genome
?
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26036
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2319
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at