chr3-138130923-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016161.3(A4GNT):c.334G>A(p.Asp112Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016161.3 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 |
---|---|---|---|---|---|---|---|---|
A4GNT | NM_016161.3 | c.334G>A | p.Asp112Asn | missense_variant | 2/3 | ENST00000236709.4 | NP_057245.1 | |
A4GNT | XM_017006543.3 | c.334G>A | p.Asp112Asn | missense_variant | 2/3 | XP_016862032.1 | ||
A4GNT | XM_017006544.2 | c.334G>A | p.Asp112Asn | missense_variant | 2/3 | XP_016862033.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
A4GNT | ENST00000236709.4 | c.334G>A | p.Asp112Asn | missense_variant | 2/3 | 1 | NM_016161.3 | ENSP00000236709.3 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251462Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135900
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461886Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727244
GnomAD4 genome AF: 0.000138 AC: 21AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.334G>A (p.D112N) alteration is located in exon 2 (coding exon 1) of the A4GNT gene. This alteration results from a G to A substitution at nucleotide position 334, causing the aspartic acid (D) at amino acid position 112 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