4-1814530-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_012318.3(LETM1):c.2114G>A(p.Ser705Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012318.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LETM1 | NM_012318.3 | c.2114G>A | p.Ser705Asn | missense_variant | Exon 14 of 14 | ENST00000302787.3 | NP_036450.1 | |
LETM1 | XM_006713884.2 | c.2111G>A | p.Ser704Asn | missense_variant | Exon 14 of 14 | XP_006713947.1 | ||
LETM1 | XM_047415673.1 | c.1571G>A | p.Ser524Asn | missense_variant | Exon 13 of 13 | XP_047271629.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152278Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249278Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134884
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461530Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727016
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152278Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74400
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2114G>A (p.S705N) alteration is located in exon 14 (coding exon 14) of the LETM1 gene. This alteration results from a G to A substitution at nucleotide position 2114, causing the serine (S) at amino acid position 705 to be replaced by an asparagine (N). 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