14-96392205-C-A

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.315
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AK7NM_152327.5 linkc.51C>A p.Thr17Thr synonymous_variant Exon 1 of 18 ENST00000267584.9 NP_689540.2 Q96M32

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AK7ENST00000267584.9 linkc.51C>A p.Thr17Thr synonymous_variant Exon 1 of 18 1 NM_152327.5 ENSP00000267584.4 Q96M32
AK7ENST00000555570.1 linkc.51C>A p.Thr17Thr synonymous_variant Exon 1 of 2 2 ENSP00000451068.1 G3V365
AK7ENST00000556643.1 linkn.62C>A non_coding_transcript_exon_variant Exon 1 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.00869
AC:
1322
AN:
152196
Hom.:
22
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0300
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00301
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.00223
AC:
560
AN:
251256
Hom.:
9
AF XY:
0.00154
AC XY:
209
AN XY:
135850
show subpopulations
Gnomad AFR exome
AF:
0.0307
Gnomad AMR exome
AF:
0.00116
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000229
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000440
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.000943
AC:
1378
AN:
1461438
Hom.:
24
Cov.:
30
AF XY:
0.000794
AC XY:
577
AN XY:
727058
show subpopulations
Gnomad4 AFR exome
AF:
0.0334
Gnomad4 AMR exome
AF:
0.00136
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000220
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000261
Gnomad4 OTH exome
AF:
0.00245
GnomAD4 genome
AF:
0.00871
AC:
1327
AN:
152314
Hom.:
22
Cov.:
31
AF XY:
0.00814
AC XY:
606
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.0300
Gnomad4 AMR
AF:
0.00301
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00993
Alfa
AF:
0.00349
Hom.:
3
Bravo
AF:
0.00992
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.30
CADD
Benign
6.3
DANN
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs111419100; hg19: chr14-96858542; API