NM_058246.4:c.948G>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_058246.4(DNAJB6):c.948G>A(p.Ser316Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,613,898 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_058246.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJB6 | ENST00000262177.9 | c.948G>A | p.Ser316Ser | synonymous_variant | Exon 10 of 10 | 1 | NM_058246.4 | ENSP00000262177.4 | ||
DNAJB6 | ENST00000459889.5 | n.*5471G>A | non_coding_transcript_exon_variant | Exon 10 of 10 | 1 | ENSP00000488263.1 | ||||
DNAJB6 | ENST00000459889.5 | n.*5471G>A | 3_prime_UTR_variant | Exon 10 of 10 | 1 | ENSP00000488263.1 | ||||
DNAJB6 | ENST00000443280.5 | c.603G>A | p.Ser201Ser | synonymous_variant | Exon 7 of 7 | 2 | ENSP00000396267.1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000410 AC: 103AN: 251048Hom.: 1 AF XY: 0.000545 AC XY: 74AN XY: 135718
GnomAD4 exome AF: 0.000214 AC: 313AN: 1461570Hom.: 5 Cov.: 32 AF XY: 0.000297 AC XY: 216AN XY: 727084
GnomAD4 genome AF: 0.000158 AC: 24AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74488
ClinVar
Submissions by phenotype
Autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6) Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:1
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Limb-Girdle Muscular Dystrophy, Dominant Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at