9-6532760-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000170.3(GLDC):c.*257G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00427 in 473,368 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000170.3 3_prime_UTR
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: 0.00972 AC: 1479AN: 152140Hom.: 28 Cov.: 32
GnomAD4 exome AF: 0.00168 AC: 538AN: 321110Hom.: 9 Cov.: 0 AF XY: 0.00140 AC XY: 238AN XY: 170608
GnomAD4 genome AF: 0.00975 AC: 1485AN: 152258Hom.: 28 Cov.: 32 AF XY: 0.00951 AC XY: 708AN XY: 74432
ClinVar
Submissions by phenotype
Glycine encephalopathy Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at