chrX-74421510-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006517.5(SLC16A2):c.-128A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000287 in 905,672 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 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_006517.5 5_prime_UTR
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: 0.0000181 AC: 2AN: 110684Hom.: 0 Cov.: 23 AF XY: 0.0000303 AC XY: 1AN XY: 32974
GnomAD3 exomes AF: 0.0000260 AC: 3AN: 115298Hom.: 0 AF XY: 0.0000265 AC XY: 1AN XY: 37782
GnomAD4 exome AF: 0.0000302 AC: 24AN: 794988Hom.: 0 Cov.: 14 AF XY: 0.0000272 AC XY: 6AN XY: 220338
GnomAD4 genome AF: 0.0000181 AC: 2AN: 110684Hom.: 0 Cov.: 23 AF XY: 0.0000303 AC XY: 1AN XY: 32974
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.95A>G (p.E32G) alteration is located in exon 1 (coding exon 1) of the SLC16A2 gene. This alteration results from a A to G substitution at nucleotide position 95, causing the glutamic acid (E) at amino acid position 32 to be replaced by a glycine (G). 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