3-38039479-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007335.4(DLEC1):c.254C>T(p.Ser85Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000372 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007335.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLEC1 | ENST00000308059.11 | c.254C>T | p.Ser85Phe | missense_variant | Exon 1 of 37 | 1 | NM_007335.4 | ENSP00000308597.6 | ||
DLEC1 | ENST00000346219.7 | c.254C>T | p.Ser85Phe | missense_variant | Exon 1 of 36 | 1 | ENSP00000315914.5 | |||
DLEC1 | ENST00000440294.6 | n.275C>T | non_coding_transcript_exon_variant | Exon 1 of 17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152288Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248864Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135154
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461646Hom.: 0 Cov.: 59 AF XY: 0.0000426 AC XY: 31AN XY: 727136
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152288Hom.: 0 Cov.: 35 AF XY: 0.0000134 AC XY: 1AN XY: 74410
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.254C>T (p.S85F) alteration is located in exon 1 (coding exon 1) of the DLEC1 gene. This alteration results from a C to T substitution at nucleotide position 254, causing the serine (S) at amino acid position 85 to be replaced by a phenylalanine (F). 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