12-4744540-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_017417.2(GALNT8):c.700G>A(p.Glu234Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000883 in 1,610,838 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_017417.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT8 | NM_017417.2 | c.700G>A | p.Glu234Lys | missense_variant | 4/11 | ENST00000252318.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT8 | ENST00000252318.7 | c.700G>A | p.Glu234Lys | missense_variant | 4/11 | 1 | NM_017417.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00457 AC: 695AN: 152166Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00120 AC: 298AN: 248804Hom.: 2 AF XY: 0.000996 AC XY: 134AN XY: 134548
GnomAD4 exome AF: 0.000496 AC: 724AN: 1458554Hom.: 4 Cov.: 29 AF XY: 0.000478 AC XY: 347AN XY: 725650
GnomAD4 genome ? AF: 0.00459 AC: 699AN: 152284Hom.: 10 Cov.: 32 AF XY: 0.00418 AC XY: 311AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 11, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at