chr5-473394-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004174.4(SLC9A3):c.2502-12C>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 0.00000319 in 1,254,196 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: not found (cov: 33)
Exomes 𝑓: 0.0000032 ( 0 hom. )
Consequence
SLC9A3
NM_004174.4 splice_polypyrimidine_tract, intron
NM_004174.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00002383
2
Clinical Significance
Conservation
PhyloP100: -1.83
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]
Genome browser will be placed here
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=-0.92).
BP6
?
Variant 5-473394-G-A is Benign according to our data. Variant chr5-473394-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1923367.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.2502-12C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000264938.8 | |||
SLC9A3-AS1 | NR_125375.1 | n.159G>A | non_coding_transcript_exon_variant | 1/7 | |||
SLC9A3 | NM_001284351.3 | c.2475-12C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.2502-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004174.4 | P2 | |||
SLC9A3 | ENST00000514375.1 | c.2475-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SLC9A3-AS1 | ENST00000607286.5 | n.159G>A | non_coding_transcript_exon_variant | 1/7 | 5 | ||||
SLC9A3 | ENST00000644203.1 | c.2252-12C>T | splice_polypyrimidine_tract_variant, intron_variant | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome AF: 0.00000319 AC: 4AN: 1254196Hom.: 0 Cov.: 31 AF XY: 0.00000162 AC XY: 1AN XY: 617660
GnomAD4 exome
AF:
AC:
4
AN:
1254196
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
617660
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
Bravo
AF:
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 | Jan 23, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
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