rs660594
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_025257.3(SLC44A4):c.1130+72C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 1,314,934 control chromosomes in the GnomAD database, including 217,701 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.60 ( 27963 hom., cov: 33)
Exomes 𝑓: 0.56 ( 189738 hom. )
Consequence
SLC44A4
NM_025257.3 intron
NM_025257.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.435
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 6-31869473-G-A is Benign according to our data. Variant chr6-31869473-G-A is described in ClinVar as [Benign]. Clinvar id is 1281145.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC44A4 | NM_025257.3 | c.1130+72C>T | intron_variant | ENST00000229729.11 | |||
SLC44A4 | NM_001178044.2 | c.1004+72C>T | intron_variant | ||||
SLC44A4 | NM_001178045.2 | c.902+72C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A4 | ENST00000229729.11 | c.1130+72C>T | intron_variant | 1 | NM_025257.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.600 AC: 91184AN: 151954Hom.: 27936 Cov.: 33
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GnomAD4 exome AF: 0.565 AC: 656844AN: 1162864Hom.: 189738 Cov.: 16 AF XY: 0.571 AC XY: 333483AN XY: 584050
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GnomAD4 genome ? AF: 0.600 AC: 91270AN: 152070Hom.: 27963 Cov.: 33 AF XY: 0.597 AC XY: 44365AN XY: 74342
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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 | GeneDx | May 15, 2021 | - - |
Computational scores
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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