19-1863179-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031918.4(KLF16):c.319G>T(p.Ala107Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,217,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031918.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLF16 | NM_031918.4 | c.319G>T | p.Ala107Ser | missense_variant | 1/2 | ENST00000250916.6 | NP_114124.1 | |
KLF16 | XM_047439498.1 | c.428-8419G>T | intron_variant | XP_047295454.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLF16 | ENST00000250916.6 | c.319G>T | p.Ala107Ser | missense_variant | 1/2 | 1 | NM_031918.4 | ENSP00000250916.3 | ||
KLF16 | ENST00000617223.1 | c.319G>T | p.Ala107Ser | missense_variant | 1/3 | 1 | ENSP00000483701.1 | |||
KLF16 | ENST00000541015.5 | n.319G>T | non_coding_transcript_exon_variant | 1/3 | 1 | ENSP00000439973.1 |
Frequencies
GnomAD3 genomes AF: 0.0000137 AC: 2AN: 146084Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000975 AC: 3AN: 30756Hom.: 0 AF XY: 0.000118 AC XY: 2AN XY: 16906
GnomAD4 exome AF: 0.00000747 AC: 8AN: 1071602Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 7AN XY: 517860
GnomAD4 genome AF: 0.0000137 AC: 2AN: 146180Hom.: 0 Cov.: 30 AF XY: 0.0000140 AC XY: 1AN XY: 71288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.319G>T (p.A107S) alteration is located in exon 1 (coding exon 1) of the KLF16 gene. This alteration results from a G to T substitution at nucleotide position 319, causing the alanine (A) at amino acid position 107 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