5-473387-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.2502-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000159 in 1,258,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004174.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.2502-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000264938.8 | |||
SLC9A3-AS1 | NR_125375.1 | n.152G>A | non_coding_transcript_exon_variant | 1/7 | |||
SLC9A3 | NM_001284351.3 | c.2475-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.2502-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004174.4 | P2 | |||
SLC9A3 | ENST00000514375.1 | c.2475-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SLC9A3-AS1 | ENST00000607286.5 | n.152G>A | non_coding_transcript_exon_variant | 1/7 | 5 | ||||
SLC9A3 | ENST00000644203.1 | c.2252-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | A2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.00000159 AC: 2AN: 1258354Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 619992
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at