X-154488194-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_019848.5(SLC10A3):c.747G>A(p.Met249Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,210,084 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112420Hom.: 0 Cov.: 24 AF XY: 0.0000289 AC XY: 1AN XY: 34580
GnomAD3 exomes AF: 0.0000874 AC: 16AN: 183146Hom.: 0 AF XY: 0.0000442 AC XY: 3AN XY: 67840
GnomAD4 exome AF: 0.0000155 AC: 17AN: 1097664Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 3AN XY: 363310
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112420Hom.: 0 Cov.: 24 AF XY: 0.0000289 AC XY: 1AN XY: 34580
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.747G>A (p.M249I) 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 747, causing the methionine (M) at amino acid position 249 to be replaced by an isoleucine (I). 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