X-154487989-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_019848.5(SLC10A3):c.952G>A(p.Val318Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,209,702 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 30 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019848.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000447 AC: 5AN: 111915Hom.: 0 Cov.: 24 AF XY: 0.0000587 AC XY: 2AN XY: 34089
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183110Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67848
GnomAD4 exome AF: 0.0000501 AC: 55AN: 1097732Hom.: 0 Cov.: 31 AF XY: 0.0000771 AC XY: 28AN XY: 363360
GnomAD4 genome AF: 0.0000447 AC: 5AN: 111970Hom.: 0 Cov.: 24 AF XY: 0.0000586 AC XY: 2AN XY: 34154
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.952G>A (p.V318M) alteration is located in exon 2 (coding exon 1) of the SLC10A3 gene. This alteration results from a G to A substitution at nucleotide position 952, causing the valine (V) at amino acid position 318 to be replaced by a methionine (M). 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