10-91840723-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_025235.4(TNKS2):c.1673+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 1,601,052 control chromosomes in the GnomAD database, including 8,569 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.094 ( 763 hom., cov: 32)
Exomes 𝑓: 0.096 ( 7806 hom. )
Consequence
TNKS2
NM_025235.4 intron
NM_025235.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.201
Genes affected
TNKS2 (HGNC:15677): (tankyrase 2) Enables NAD+ ADP-ribosyltransferase activity; enzyme binding activity; and protein ADP-ribosylase activity. Involved in several processes, including protein ADP-ribosylation; protein localization to chromosome, telomeric region; and regulation of telomere maintenance. Located in nuclear envelope; pericentriolar material; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 10-91840723-G-A is Benign according to our data. Variant chr10-91840723-G-A is described in ClinVar as [Benign]. Clinvar id is 1335822.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNKS2 | NM_025235.4 | c.1673+17G>A | intron_variant | ENST00000371627.5 | NP_079511.1 | |||
TNKS2 | XM_011540213.2 | c.1736+17G>A | intron_variant | XP_011538515.1 | ||||
TNKS2 | XM_017016699.2 | c.1352+17G>A | intron_variant | XP_016872188.1 | ||||
TNKS2 | XM_017016700.3 | c.377+17G>A | intron_variant | XP_016872189.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNKS2 | ENST00000371627.5 | c.1673+17G>A | intron_variant | 1 | NM_025235.4 | ENSP00000360689 | P1 | |||
TNKS2 | ENST00000710380.1 | c.1712+17G>A | intron_variant | ENSP00000518237 |
Frequencies
GnomAD3 genomes AF: 0.0942 AC: 14320AN: 152042Hom.: 759 Cov.: 32
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GnomAD3 exomes AF: 0.120 AC: 29410AN: 244542Hom.: 2218 AF XY: 0.119 AC XY: 15684AN XY: 132188
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GnomAD4 exome AF: 0.0961 AC: 139247AN: 1448892Hom.: 7806 Cov.: 30 AF XY: 0.0978 AC XY: 70378AN XY: 719926
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GnomAD4 genome AF: 0.0942 AC: 14328AN: 152160Hom.: 763 Cov.: 32 AF XY: 0.0970 AC XY: 7220AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 21, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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