12-57626799-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001478.5(B4GALNT1):c.1547C>T(p.Ala516Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00961 in 1,614,208 control chromosomes in the GnomAD database, including 89 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 (★★).
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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00736 AC: 1120AN: 152204Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00741 AC: 1864AN: 251486Hom.: 16 AF XY: 0.00734 AC XY: 998AN XY: 135916
GnomAD4 exome AF: 0.00985 AC: 14401AN: 1461886Hom.: 86 Cov.: 31 AF XY: 0.00971 AC XY: 7062AN XY: 727246
GnomAD4 genome AF: 0.00735 AC: 1119AN: 152322Hom.: 3 Cov.: 32 AF XY: 0.00717 AC XY: 534AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:3
B4GALNT1: BP4, BS1, BS2 -
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not specified Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at