chr14-60461410-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_174978.3(C14orf39):c.1061T>C(p.Leu354Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000332 in 1,607,468 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_174978.3 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C14orf39 | NM_174978.3 | c.1061T>C | p.Leu354Ser | missense_variant, splice_region_variant | 13/18 | ENST00000321731.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C14orf39 | ENST00000321731.8 | c.1061T>C | p.Leu354Ser | missense_variant, splice_region_variant | 13/18 | 1 | NM_174978.3 | P1 | |
C14orf39 | ENST00000557138.5 | c.*375T>C | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 8/13 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 27AN: 152086Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000265 AC: 66AN: 248890Hom.: 0 AF XY: 0.000260 AC XY: 35AN XY: 134778
GnomAD4 exome AF: 0.000348 AC: 506AN: 1455382Hom.: 2 Cov.: 29 AF XY: 0.000320 AC XY: 232AN XY: 723986
GnomAD4 genome ? AF: 0.000178 AC: 27AN: 152086Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1061T>C (p.L354S) alteration is located in exon 13 (coding exon 12) of the C14orf39 gene. This alteration results from a T to C substitution at nucleotide position 1061, causing the leucine (L) at amino acid position 354 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