NM_005866.4:c.153G>A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_005866.4(SIGMAR1):c.153G>A(p.Gly51Gly) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,602,422 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005866.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0183 AC: 2783AN: 152240Hom.: 100 Cov.: 33
GnomAD3 exomes AF: 0.00482 AC: 1100AN: 228184Hom.: 31 AF XY: 0.00353 AC XY: 444AN XY: 125656
GnomAD4 exome AF: 0.00180 AC: 2611AN: 1450064Hom.: 55 Cov.: 32 AF XY: 0.00150 AC XY: 1086AN XY: 721718
GnomAD4 genome AF: 0.0183 AC: 2790AN: 152358Hom.: 100 Cov.: 33 AF XY: 0.0175 AC XY: 1301AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
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Autosomal recessive distal spinal muscular atrophy 2;C3280587:Amyotrophic lateral sclerosis type 16 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at