3-50341197-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000231749.8(ZMYND10):c.*213T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0749 in 653,344 control chromosomes in the GnomAD database, including 8,971 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.12 ( 2767 hom., cov: 33)
Exomes 𝑓: 0.061 ( 6204 hom. )
Consequence
ZMYND10
ENST00000231749.8 3_prime_UTR
ENST00000231749.8 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.65
Genes affected
ZMYND10 (HGNC:19412): (zinc finger MYND-type containing 10) This gene encodes a protein containing a MYND-type zinc finger domain that likely functions in assembly of the dynein motor. Mutations in this gene can cause primary ciliary dyskinesia. This gene is also considered a tumor suppressor gene and is often mutated, deleted, or hypermethylated and silenced in cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
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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=-0.82).
BP6
Variant 3-50341197-A-G is Benign according to our data. Variant chr3-50341197-A-G is described in ClinVar as [Benign]. Clinvar id is 1221244.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZMYND10 | NM_015896.4 | c.*213T>C | 3_prime_UTR_variant | 12/12 | ENST00000231749.8 | NP_056980.2 | ||
ZMYND10 | NM_001308379.2 | c.*213T>C | 3_prime_UTR_variant | 11/11 | NP_001295308.1 | |||
ZMYND10 | XM_005265216.4 | c.*213T>C | 3_prime_UTR_variant | 11/11 | XP_005265273.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZMYND10 | ENST00000231749.8 | c.*213T>C | 3_prime_UTR_variant | 12/12 | 1 | NM_015896.4 | ENSP00000231749 | P1 | ||
ZMYND10-AS1 | ENST00000440013.1 | n.92A>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.119 AC: 18061AN: 152118Hom.: 2761 Cov.: 33
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GnomAD4 exome AF: 0.0615 AC: 30816AN: 501108Hom.: 6204 Cov.: 6 AF XY: 0.0566 AC XY: 14846AN XY: 262152
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GnomAD4 genome AF: 0.119 AC: 18123AN: 152236Hom.: 2767 Cov.: 33 AF XY: 0.125 AC XY: 9289AN XY: 74444
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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 | Nov 13, 2018 | - - |
Computational scores
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BayesDel_noAF
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