chr17-36493933-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004773.4(ZNHIT3):āc.213T>Cā(p.Asp71=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000231 in 1,612,828 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00021 ( 0 hom., cov: 33)
Exomes š: 0.00023 ( 3 hom. )
Consequence
ZNHIT3
NM_004773.4 synonymous
NM_004773.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.78
Genes affected
ZNHIT3 (HGNC:12309): (zinc finger HIT-type containing 3) Predicted to enable thyroid hormone receptor binding activity. Predicted to be involved in box C/D snoRNP assembly; maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); and snoRNA localization. Located in cytoplasm and nucleus. Implicated in PEHO syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 17-36493933-T-C is Benign according to our data. Variant chr17-36493933-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 726269.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.78 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNHIT3 | NM_004773.4 | c.213T>C | p.Asp71= | synonymous_variant | 4/5 | ENST00000617429.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNHIT3 | ENST00000617429.5 | c.213T>C | p.Asp71= | synonymous_variant | 4/5 | 1 | NM_004773.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152206Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000530 AC: 133AN: 250998Hom.: 1 AF XY: 0.000501 AC XY: 68AN XY: 135638
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GnomAD4 exome AF: 0.000233 AC: 340AN: 1460622Hom.: 3 Cov.: 29 AF XY: 0.000223 AC XY: 162AN XY: 726698
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GnomAD4 genome AF: 0.000210 AC: 32AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at