chr10-96370242-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012465.4(TLL2):c.2736C>T(p.Asn912=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00449 in 1,613,526 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0046 ( 21 hom. )
Consequence
TLL2
NM_012465.4 synonymous
NM_012465.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.36
Genes affected
TLL2 (HGNC:11844): (tolloid like 2) This gene encodes an astacin-like zinc-dependent metalloprotease and is a subfamily member of the metzincin family. Unlike other family members, a similar protein in mice does not cleave procollagen C-propeptides or chordin. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 10-96370242-G-A is Benign according to our data. Variant chr10-96370242-G-A is described in ClinVar as [Benign]. Clinvar id is 714624.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLL2 | NM_012465.4 | c.2736C>T | p.Asn912= | synonymous_variant | 20/21 | ENST00000357947.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLL2 | ENST00000357947.4 | c.2736C>T | p.Asn912= | synonymous_variant | 20/21 | 1 | NM_012465.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00362 AC: 551AN: 152264Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00431 AC: 1077AN: 250160Hom.: 5 AF XY: 0.00419 AC XY: 567AN XY: 135190
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GnomAD4 exome AF: 0.00458 AC: 6690AN: 1461144Hom.: 21 Cov.: 31 AF XY: 0.00444 AC XY: 3227AN XY: 726830
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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 | Invitae | Jan 31, 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