5-473400-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004174.4(SLC9A3):c.2502-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,396,332 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 0.000053 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
SLC9A3
NM_004174.4 intron
NM_004174.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.772
Genes affected
SLC9A3 (HGNC:11073): (solute carrier family 9 member A3) The protein encoded by this gene is an epithelial brush border Na/H exchanger that uses an inward sodium ion gradient to expel acids from the cell. Defects in this gene are a cause of congenital secretory sodium diarrhea. Pseudogenes of this gene exist on chromosomes 10 and 22. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 5-473400-G-A is Benign according to our data. Variant chr5-473400-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1644088.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.2502-18C>T | intron_variant | ENST00000264938.8 | |||
SLC9A3-AS1 | NR_125375.1 | n.164+1G>A | splice_donor_variant, non_coding_transcript_variant | ||||
SLC9A3 | NM_001284351.3 | c.2475-18C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.2502-18C>T | intron_variant | 1 | NM_004174.4 | P2 | |||
SLC9A3 | ENST00000514375.1 | c.2475-18C>T | intron_variant | 1 | |||||
SLC9A3-AS1 | ENST00000607286.5 | n.164+1G>A | splice_donor_variant, non_coding_transcript_variant | 5 | |||||
SLC9A3 | ENST00000644203.1 | c.2252-18C>T | intron_variant | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000528 AC: 8AN: 151476Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000139 AC: 10AN: 71712Hom.: 0 AF XY: 0.0000960 AC XY: 4AN XY: 41674
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GnomAD4 exome AF: 0.000135 AC: 168AN: 1244856Hom.: 0 Cov.: 31 AF XY: 0.000129 AC XY: 79AN XY: 612274
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GnomAD4 genome AF: 0.0000528 AC: 8AN: 151476Hom.: 0 Cov.: 34 AF XY: 0.0000540 AC XY: 4AN XY: 74018
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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 | Invitae | Dec 13, 2023 | - - |
Computational scores
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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