chr16-23478894-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015044.4(GGA2):c.1147G>A(p.Val383Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000688 in 1,453,998 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 (★).
Frequency
Consequence
NM_015044.4 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 |
---|---|---|---|---|---|---|---|
GGA2 | NM_015044.4 | c.1147G>A | p.Val383Ile | missense_variant | 12/17 | ENST00000309859.8 | |
GGA2 | XM_047433801.1 | c.1117G>A | p.Val373Ile | missense_variant | 13/18 | ||
GGA2 | XM_047433802.1 | c.1036G>A | p.Val346Ile | missense_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GGA2 | ENST00000309859.8 | c.1147G>A | p.Val383Ile | missense_variant | 12/17 | 1 | NM_015044.4 | P1 | |
GGA2 | ENST00000567468.5 | c.624+7852G>A | intron_variant | 2 | |||||
GGA2 | ENST00000569182.1 | n.333G>A | non_coding_transcript_exon_variant | 3/5 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250500Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135430
GnomAD4 exome AF: 0.00000688 AC: 10AN: 1453998Hom.: 0 Cov.: 28 AF XY: 0.00000829 AC XY: 6AN XY: 723874
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at