11-63764893-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001144936.2(ZFTA):c.999G>A(p.Leu333Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000408 in 1,519,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
ZFTA
NM_001144936.2 synonymous
NM_001144936.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00300
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 11-63764893-C-T is Benign according to our data. Variant chr11-63764893-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641902.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.003 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFTA | NM_001144936.2 | c.999G>A | p.Leu333Leu | synonymous_variant | Exon 3 of 5 | ENST00000433688.2 | NP_001138408.1 | |
ZFTA | XM_047427478.1 | c.999G>A | p.Leu333Leu | synonymous_variant | Exon 3 of 4 | XP_047283434.1 | ||
ZFTA | XM_047427477.1 | c.638-295G>A | intron_variant | Intron 2 of 3 | XP_047283433.1 | |||
ZFTA | XM_024448662.2 | c.637+914G>A | intron_variant | Intron 2 of 2 | XP_024304430.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFTA | ENST00000433688.2 | c.999G>A | p.Leu333Leu | synonymous_variant | Exon 3 of 5 | 5 | NM_001144936.2 | ENSP00000482180.1 | ||
ZFTA | ENST00000338498.6 | c.154+914G>A | intron_variant | Intron 1 of 1 | 1 | ENSP00000483097.1 | ||||
ZFTA | ENST00000445014.3 | c.384G>A | p.Leu128Leu | synonymous_variant | Exon 3 of 4 | 5 | ENSP00000478462.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000166 AC: 19AN: 114802Hom.: 0 AF XY: 0.000176 AC XY: 11AN XY: 62454
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GnomAD4 exome AF: 0.0000395 AC: 54AN: 1367252Hom.: 0 Cov.: 31 AF XY: 0.0000416 AC XY: 28AN XY: 672558
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GnomAD4 genome AF: 0.0000525 AC: 8AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74456
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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
Jan 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
ZFTA: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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