rs11703570
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000355.4(TCN2):c.427+89T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,535,186 control chromosomes in the GnomAD database, including 38,586 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.22 ( 3657 hom., cov: 32)
Exomes 𝑓: 0.22 ( 34929 hom. )
Consequence
TCN2
NM_000355.4 intron
NM_000355.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.368
Genes affected
TCN2 (HGNC:11653): (transcobalamin 2) This gene encodes a member of the vitamin B12-binding protein family. This family of proteins, alternatively referred to as R binders, is expressed in various tissues and secretions. This plasma protein binds cobalamin and mediates the transport of cobalamin into cells. This protein and other mammalian cobalamin-binding proteins, such as transcobalamin I and gastric intrisic factor, may have evolved by duplication of a common ancestral gene. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 22-30613131-T-A is Benign according to our data. Variant chr22-30613131-T-A is described in ClinVar as [Benign]. Clinvar id is 1179882.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCN2 | NM_000355.4 | c.427+89T>A | intron_variant | ENST00000215838.8 | |||
TCN2 | NM_001184726.2 | c.346+170T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCN2 | ENST00000215838.8 | c.427+89T>A | intron_variant | 1 | NM_000355.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.219 AC: 33276AN: 151936Hom.: 3651 Cov.: 32
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GnomAD4 exome AF: 0.223 AC: 307930AN: 1383132Hom.: 34929 AF XY: 0.223 AC XY: 152657AN XY: 683938
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GnomAD4 genome ? AF: 0.219 AC: 33288AN: 152054Hom.: 3657 Cov.: 32 AF XY: 0.219 AC XY: 16271AN XY: 74334
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Computational scores
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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