chr14-60471601-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_174978.3(C14orf39):c.462A>G(p.Ala154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00621 in 1,610,426 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0064 ( 52 hom. )
Consequence
C14orf39
NM_174978.3 synonymous
NM_174978.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.47
Genes affected
C14orf39 (HGNC:19849): (chromosome 14 open reading frame 39) Predicted to be involved in gamete generation and meiosis I. Predicted to be located in chromosome. Predicted to be active in central element. Implicated in primary ovarian insufficiency 18 and spermatogenic failure 52. [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=-0.49).
BP6
?
Variant 14-60471601-T-C is Benign according to our data. Variant chr14-60471601-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2644269.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.47 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C14orf39 | NM_174978.3 | c.462A>G | p.Ala154= | synonymous_variant | 6/18 | ENST00000321731.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C14orf39 | ENST00000321731.8 | c.462A>G | p.Ala154= | synonymous_variant | 6/18 | 1 | NM_174978.3 | P1 | |
C14orf39 | ENST00000557138.5 | c.107-3068A>G | intron_variant, NMD_transcript_variant | 1 | |||||
C14orf39 | ENST00000555476.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00448 AC: 681AN: 152018Hom.: 7 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00521 AC: 1295AN: 248494Hom.: 7 AF XY: 0.00543 AC XY: 729AN XY: 134278
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GnomAD4 exome AF: 0.00639 AC: 9316AN: 1458290Hom.: 52 Cov.: 31 AF XY: 0.00651 AC XY: 4725AN XY: 725368
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GnomAD4 genome ? AF: 0.00447 AC: 680AN: 152136Hom.: 7 Cov.: 32 AF XY: 0.00376 AC XY: 280AN XY: 74382
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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 | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | C14orf39: BP4, BP7, BS2 - |
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