chr5-474924-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004174.4(SLC9A3):c.2460C>G(p.Pro820=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,576 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
Consequence
NM_004174.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.2460C>G | p.Pro820= | synonymous_variant | 16/17 | ENST00000264938.8 | |
SLC9A3-AS1 | NR_125375.1 | n.165-213G>C | intron_variant, non_coding_transcript_variant | ||||
SLC9A3 | NM_001284351.3 | c.2433C>G | p.Pro811= | synonymous_variant | 16/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.2460C>G | p.Pro820= | synonymous_variant | 16/17 | 1 | NM_004174.4 | P2 | |
SLC9A3-AS1 | ENST00000607286.5 | n.165-213G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448576Hom.: 0 Cov.: 46 AF XY: 0.00000139 AC XY: 1AN XY: 719694
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.