rs149734145
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_152490.5(B3GALNT2):āc.369T>Cā(p.Asn123=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000463 in 1,613,886 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00035 ( 1 hom., cov: 33)
Exomes š: 0.00047 ( 0 hom. )
Consequence
B3GALNT2
NM_152490.5 synonymous
NM_152490.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.51
Genes affected
B3GALNT2 (HGNC:28596): (beta-1,3-N-acetylgalactosaminyltransferase 2) This gene encodes a member of the glycosyltransferase 31 family. The encoded protein synthesizes GalNAc:beta-1,3GlcNAc, a novel carbohydrate structure, on N- and O-glycans. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Mar 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 1-235484508-A-G is Benign according to our data. Variant chr1-235484508-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 509485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-235484508-A-G is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=1.51 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B3GALNT2 | NM_152490.5 | c.369T>C | p.Asn123= | synonymous_variant | 4/12 | ENST00000366600.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GALNT2 | ENST00000366600.8 | c.369T>C | p.Asn123= | synonymous_variant | 4/12 | 1 | NM_152490.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000355 AC: 54AN: 152214Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000303 AC: 76AN: 250452Hom.: 0 AF XY: 0.000355 AC XY: 48AN XY: 135370
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GnomAD4 exome AF: 0.000475 AC: 694AN: 1461554Hom.: 0 Cov.: 32 AF XY: 0.000513 AC XY: 373AN XY: 727078
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GnomAD4 genome ? AF: 0.000354 AC: 54AN: 152332Hom.: 1 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 02, 2018 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at