chr12-57625419-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001478.5(B4GALNT1):c.*1325G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,614,136 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 13 hom. )
Consequence
B4GALNT1
NM_001478.5 3_prime_UTR
NM_001478.5 3_prime_UTR
Scores
1
3
3
Clinical Significance
Conservation
PhyloP100: 0.629
Genes affected
B4GALNT1 (HGNC:4117): (beta-1,4-N-acetyl-galactosaminyltransferase 1) GM2 and GD2 gangliosides are sialic acid-containing glycosphingolipids. GalNAc-T is the enzyme involved in the biosynthesis of G(M2) and G(D2) glycosphingolipids. GalNAc-T catalyzes the transfer of GalNAc into G(M3) and G(D3) by a beta-1,4 linkage, resulting in the synthesis of G(M2) and G(D2), respectively. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2013]
SLC26A10P (HGNC:14470): (solute carrier family 26 member 10, pseudogene) Predicted to enable anion transmembrane transporter activity. Predicted to be involved in anion transport. Predicted to be active in basolateral plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
Variant 12-57625419-C-T is Benign according to our data. Variant chr12-57625419-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1686497.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00239 (364/152260) while in subpopulation AMR AF= 0.00608 (93/15302). AF 95% confidence interval is 0.00508. There are 2 homozygotes in gnomad4. There are 171 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B4GALNT1 | NM_001478.5 | c.*1325G>A | 3_prime_UTR_variant | 11/11 | ENST00000341156.9 | ||
SLC26A10P | NR_166679.1 | n.2272C>T | non_coding_transcript_exon_variant | 14/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B4GALNT1 | ENST00000341156.9 | c.*1325G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_001478.5 | P1 | ||
ENST00000440686.5 | n.1450C>T | non_coding_transcript_exon_variant | 14/16 | 2 | |||||
SLC26A10P | ENST00000665594.1 | n.1879C>T | non_coding_transcript_exon_variant | 16/18 |
Frequencies
GnomAD3 genomes AF: 0.00239 AC: 364AN: 152142Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00237 AC: 597AN: 251456Hom.: 5 AF XY: 0.00255 AC XY: 347AN XY: 135900
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GnomAD4 exome AF: 0.00270 AC: 3941AN: 1461876Hom.: 13 Cov.: 38 AF XY: 0.00266 AC XY: 1935AN XY: 727244
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GnomAD4 genome AF: 0.00239 AC: 364AN: 152260Hom.: 2 Cov.: 32 AF XY: 0.00230 AC XY: 171AN XY: 74440
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_addAF
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T
BayesDel_noAF
Pathogenic
CADD
Benign
DANN
Uncertain
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Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
D;N
Vest4
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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