rs810205
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001478.5(B4GALNT1):āc.514G>Cā(p.Gly172Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0192 in 1,609,128 control chromosomes in the GnomAD database, including 397 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G172S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001478.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B4GALNT1 | NM_001478.5 | c.514G>C | p.Gly172Arg | missense_variant | 5/11 | ENST00000341156.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B4GALNT1 | ENST00000341156.9 | c.514G>C | p.Gly172Arg | missense_variant | 5/11 | 1 | NM_001478.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0279 AC: 4241AN: 152184Hom.: 83 Cov.: 33
GnomAD3 exomes AF: 0.0191 AC: 4719AN: 246592Hom.: 71 AF XY: 0.0188 AC XY: 2505AN XY: 133156
GnomAD4 exome AF: 0.0183 AC: 26593AN: 1456826Hom.: 313 Cov.: 32 AF XY: 0.0182 AC XY: 13168AN XY: 724394
GnomAD4 genome ? AF: 0.0279 AC: 4244AN: 152302Hom.: 84 Cov.: 33 AF XY: 0.0290 AC XY: 2156AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at