chr3-38045577-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007335.4(DLEC1):āc.446T>Cā(p.Phe149Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007335.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLEC1 | NM_007335.4 | c.446T>C | p.Phe149Ser | missense_variant | 2/37 | ENST00000308059.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLEC1 | ENST00000308059.11 | c.446T>C | p.Phe149Ser | missense_variant | 2/37 | 1 | NM_007335.4 | P2 | |
DLEC1 | ENST00000346219.7 | c.446T>C | p.Phe149Ser | missense_variant | 2/36 | 1 | A2 | ||
DLEC1 | ENST00000440294.6 | n.467T>C | non_coding_transcript_exon_variant | 2/17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249134Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135148
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461704Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727164
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.446T>C (p.F149S) alteration is located in exon 2 (coding exon 2) of the DLEC1 gene. This alteration results from a T to C substitution at nucleotide position 446, causing the phenylalanine (F) at amino acid position 149 to be replaced by a serine (S). 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