19-35313292-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_002361.4(MAG):c.1719C>T(p.Ser573Ser) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000949 in 1,612,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000098 ( 0 hom. )
Consequence
MAG
NM_002361.4 splice_region, synonymous
NM_002361.4 splice_region, synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.08
Genes affected
MAG (HGNC:6783): (myelin associated glycoprotein) The protein encoded by this gene is a type I membrane protein and member of the immunoglobulin superfamily. It is thought to be involved in the process of myelination. It is a lectin that binds to sialylated glycoconjugates and mediates certain myelin-neuron cell-cell interactions. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 19-35313292-C-T is Benign according to our data. Variant chr19-35313292-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 568410.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BP7
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000657 (10/152200) while in subpopulation NFE AF= 0.000147 (10/68020). AF 95% confidence interval is 0.0000791. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MAG | NM_002361.4 | c.1719C>T | p.Ser573Ser | splice_region_variant, synonymous_variant | Exon 11 of 11 | ENST00000392213.8 | NP_002352.1 | |
| MAG | NM_080600.3 | c.*15C>T | splice_region_variant | Exon 12 of 12 | NP_542167.1 | |||
| MAG | NM_001199216.2 | c.1644C>T | p.Ser548Ser | splice_region_variant, synonymous_variant | Exon 11 of 11 | NP_001186145.1 | ||
| MAG | NM_080600.3 | c.*15C>T | 3_prime_UTR_variant | Exon 12 of 12 | NP_542167.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MAG | ENST00000361922.8 | c.*15C>T | splice_region_variant | Exon 12 of 12 | 1 | ENSP00000355234.4 | ||||
| MAG | ENST00000392213.8 | c.1719C>T | p.Ser573Ser | splice_region_variant, synonymous_variant | Exon 11 of 11 | 1 | NM_002361.4 | ENSP00000376048.2 | ||
| MAG | ENST00000537831.2 | c.1644C>T | p.Ser548Ser | splice_region_variant, synonymous_variant | Exon 11 of 11 | 1 | ENSP00000440695.1 | |||
| MAG | ENST00000361922.8 | c.*15C>T | 3_prime_UTR_variant | Exon 12 of 12 | 1 | ENSP00000355234.4 |
Frequencies
GnomAD3 genomes 0.0000657 AC: 10AN: 152200Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248986Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134656
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GnomAD4 exome AF: 0.0000979 AC: 143AN: 1460326Hom.: 0 Cov.: 31 AF XY: 0.0000757 AC XY: 55AN XY: 726502
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GnomAD4 genome 0.0000657 AC: 10AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74348
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Hereditary spastic paraplegia 75 Benign:1
Jan 28, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at