chrX-74421529-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006517.5(SLC16A2):c.-109C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000591 in 1,015,519 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000269 AC: 3AN: 111581Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33813
GnomAD3 exomes AF: 0.00000843 AC: 1AN: 118650Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 37762
GnomAD4 exome AF: 0.00000332 AC: 3AN: 903938Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0AN XY: 255120
GnomAD4 genome AF: 0.0000269 AC: 3AN: 111581Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33813
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.114C>A (p.S38R) alteration is located in exon 1 (coding exon 1) of the SLC16A2 gene. This alteration results from a C to A substitution at nucleotide position 114, causing the serine (S) at amino acid position 38 to be replaced by an arginine (R). 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