14-96392205-C-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_152327.5(AK7):c.51C>A(p.Thr17Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00168 in 1,613,752 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0087 ( 22 hom., cov: 31)
Exomes 𝑓: 0.00094 ( 24 hom. )
Consequence
AK7
NM_152327.5 synonymous
NM_152327.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.315
Genes affected
AK7 (HGNC:20091): (adenylate kinase 7) This gene encodes a member of the adenylate kinase family of enzymes. The encoded enzyme is a phosphotransferase that catalyzes the reversible phosphorylation of adenine nucleotides. This enzyme plays a role in energy homeostasis of the cell. Alternative splicing results in multiple transcript variants. Mutations in the mouse gene are associated with primary ciliary dyskinesia. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
Variant 14-96392205-C-A is Benign according to our data. Variant chr14-96392205-C-A is described in ClinVar as [Benign]. Clinvar id is 1653243.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.315 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00871 (1327/152314) while in subpopulation AFR AF= 0.03 (1247/41570). AF 95% confidence interval is 0.0286. There are 22 homozygotes in gnomad4. There are 606 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 22 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AK7 | ENST00000267584.9 | c.51C>A | p.Thr17Thr | synonymous_variant | Exon 1 of 18 | 1 | NM_152327.5 | ENSP00000267584.4 | ||
AK7 | ENST00000555570.1 | c.51C>A | p.Thr17Thr | synonymous_variant | Exon 1 of 2 | 2 | ENSP00000451068.1 | |||
AK7 | ENST00000556643.1 | n.62C>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00869 AC: 1322AN: 152196Hom.: 22 Cov.: 31
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GnomAD3 exomes AF: 0.00223 AC: 560AN: 251256Hom.: 9 AF XY: 0.00154 AC XY: 209AN XY: 135850
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GnomAD4 exome AF: 0.000943 AC: 1378AN: 1461438Hom.: 24 Cov.: 30 AF XY: 0.000794 AC XY: 577AN XY: 727058
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GnomAD4 genome AF: 0.00871 AC: 1327AN: 152314Hom.: 22 Cov.: 31 AF XY: 0.00814 AC XY: 606AN XY: 74466
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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
Feb 02, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
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