19-17489115-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_198580.3(SLC27A1):āc.994A>Gā(p.Thr332Ala) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000124 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_198580.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC27A1 | NM_198580.3 | c.994A>G | p.Thr332Ala | missense_variant, splice_region_variant | 6/12 | ENST00000252595.12 | NP_940982.1 | |
PGLS-DT | NR_147835.1 | n.670-20T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC27A1 | ENST00000252595.12 | c.994A>G | p.Thr332Ala | missense_variant, splice_region_variant | 6/12 | 1 | NM_198580.3 | ENSP00000252595 | P1 | |
PGLS-DT | ENST00000596643.5 | n.670-20T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461678Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727144
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 19, 2024 | The c.994A>G (p.T332A) alteration is located in exon 6 (coding exon 6) of the SLC27A1 gene. This alteration results from a A to G substitution at nucleotide position 994, causing the threonine (T) at amino acid position 332 to be replaced by an alanine (A). 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