4-48483584-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152679.4(SLC10A4):c.23C>A(p.Thr8Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,506,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152679.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC10A4 | NM_152679.4 | c.23C>A | p.Thr8Asn | missense_variant | 1/3 | ENST00000273861.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC10A4 | ENST00000273861.5 | c.23C>A | p.Thr8Asn | missense_variant | 1/3 | 1 | NM_152679.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151884Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000180 AC: 2AN: 111418Hom.: 0 AF XY: 0.0000320 AC XY: 2AN XY: 62504
GnomAD4 exome AF: 0.0000207 AC: 28AN: 1355062Hom.: 0 Cov.: 31 AF XY: 0.0000164 AC XY: 11AN XY: 669818
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151884Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74184
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.23C>A (p.T8N) alteration is located in exon 1 (coding exon 1) of the SLC10A4 gene. This alteration results from a C to A substitution at nucleotide position 23, causing the threonine (T) at amino acid position 8 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at