chr2-30942270-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024572.4(GALNT14):c.862G>A(p.Asp288Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000849 in 1,613,954 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_024572.4 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 |
---|---|---|---|---|---|---|---|
GALNT14 | NM_024572.4 | c.862G>A | p.Asp288Asn | missense_variant | 9/15 | ENST00000349752.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT14 | ENST00000349752.10 | c.862G>A | p.Asp288Asn | missense_variant | 9/15 | 1 | NM_024572.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000215 AC: 54AN: 251400Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135870
GnomAD4 exome AF: 0.0000848 AC: 124AN: 1461804Hom.: 0 Cov.: 30 AF XY: 0.000109 AC XY: 79AN XY: 727210
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.862G>A (p.D288N) alteration is located in exon 9 (coding exon 9) of the GALNT14 gene. This alteration results from a G to A substitution at nucleotide position 862, causing the aspartic acid (D) at amino acid position 288 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