rs767016855
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 12P and 1B. PVS1PM2PP3_ModerateBS1_Supporting
The NM_000337.6(SGCD):c.-43-1G>A variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000808 in 1,609,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000337.6 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGCD | NM_000337.6 | c.-43-1G>A | splice_acceptor_variant | ENST00000337851.9 | |||
LOC124901120 | XR_007059016.1 | n.234+17920C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGCD | ENST00000337851.9 | c.-43-1G>A | splice_acceptor_variant | 1 | NM_000337.6 | P4 | |||
SGCD | ENST00000435422.7 | c.-1+2301G>A | intron_variant | 1 | A1 | ||||
SGCD | ENST00000517913.5 | c.-43-1G>A | splice_acceptor_variant | 5 | |||||
SGCD | ENST00000524347.2 | c.-43-1G>A | splice_acceptor_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248858Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135022
GnomAD4 exome AF: 0.00000618 AC: 9AN: 1456952Hom.: 0 Cov.: 28 AF XY: 0.00000414 AC XY: 3AN XY: 725204
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2F;C1847667:Dilated cardiomyopathy 1L Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 14, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Dec 08, 2017 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 22, 2021 | - - |
Uncertain significance, criteria provided, single submitter | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jun 24, 2013 | - - |
Autosomal recessive limb-girdle muscular dystrophy type 2F Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Dilated cardiomyopathy 1L Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at