14-81499512-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005065.6(SEL1L):c.838G>A(p.Val280Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,611,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005065.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEL1L | NM_005065.6 | c.838G>A | p.Val280Ile | missense_variant | 8/21 | ENST00000336735.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEL1L | ENST00000336735.9 | c.838G>A | p.Val280Ile | missense_variant | 8/21 | 1 | NM_005065.6 | P1 | |
SEL1L | ENST00000555824.5 | c.838G>A | p.Val280Ile | missense_variant | 8/8 | 1 | |||
SEL1L | ENST00000554744.1 | n.412G>A | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152116Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249346Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134768
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1459518Hom.: 0 Cov.: 32 AF XY: 0.0000262 AC XY: 19AN XY: 726002
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152116Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.838G>A (p.V280I) alteration is located in exon 1 (coding exon 1) of the SEL1L gene. This alteration results from a G to A substitution at nucleotide position 838, causing the valine (V) at amino acid position 280 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