rs614549
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025257.3(SLC44A4):c.530-1287T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,544 control chromosomes in the GnomAD database, including 12,099 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 0.40 ( 12099 hom., cov: 32)
Consequence
SLC44A4
NM_025257.3 intron
NM_025257.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.61
Genes affected
SLC44A4 (HGNC:13941): (solute carrier family 44 member 4) The protein encoded by this gene may be a sodium-dependent transmembrane transport protein involved in the uptake of choline by cholinergic neurons. Defects in this gene can cause sialidosis, a lysosomal storage disease. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
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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 (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC44A4 | NM_025257.3 | c.530-1287T>C | intron_variant | ENST00000229729.11 | |||
SLC44A4 | NM_001178044.2 | c.404-1287T>C | intron_variant | ||||
SLC44A4 | NM_001178045.2 | c.302-1287T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A4 | ENST00000229729.11 | c.530-1287T>C | intron_variant | 1 | NM_025257.3 | P1 | |||
SLC44A4 | ENST00000375562.8 | c.404-1287T>C | intron_variant | 2 | |||||
SLC44A4 | ENST00000414427.1 | c.517-1287T>C | intron_variant | 5 | |||||
SLC44A4 | ENST00000544672.5 | c.302-1287T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.395 AC: 59884AN: 151422Hom.: 12090 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.396 AC: 59938AN: 151544Hom.: 12099 Cov.: 32 AF XY: 0.394 AC XY: 29181AN XY: 74016
GnomAD4 genome
?
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32
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29181
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74016
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1258
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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