chr5-139372262-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005847.5(SLC23A1):c.1550-9C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00232 in 1,607,672 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 23 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 31 hom. )
Consequence
SLC23A1
NM_005847.5 splice_polypyrimidine_tract, intron
NM_005847.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0003133
2
Clinical Significance
Conservation
PhyloP100: 1.20
Genes affected
SLC23A1 (HGNC:10974): (solute carrier family 23 member 1) The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two transporters. The encoded protein is active in bulk vitamin C transport involving epithelial surfaces. Previously, this gene had an official symbol of SLC23A2. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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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=-0.72).
BP6
?
Variant 5-139372262-G-A is Benign according to our data. Variant chr5-139372262-G-A is described in ClinVar as [Benign]. Clinvar id is 785138.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0114 (1733/152296) while in subpopulation AFR AF= 0.0389 (1616/41556). AF 95% confidence interval is 0.0373. There are 23 homozygotes in gnomad4. There are 776 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC23A1 | NM_005847.5 | c.1550-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000348729.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC23A1 | ENST00000348729.8 | c.1550-9C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005847.5 | P1 | |||
SLC23A1 | ENST00000353963.7 | c.1562-9C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1732AN: 152178Hom.: 23 Cov.: 32
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GnomAD3 exomes AF: 0.00334 AC: 831AN: 248644Hom.: 15 AF XY: 0.00228 AC XY: 308AN XY: 134874
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GnomAD4 exome AF: 0.00137 AC: 1997AN: 1455376Hom.: 31 Cov.: 31 AF XY: 0.00119 AC XY: 857AN XY: 723128
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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 | Jul 23, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at