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GeneBe

6-109497503-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001145128.3(AK9):c.5277T>C(p.Tyr1759=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00527 in 1,608,172 control chromosomes in the GnomAD database, including 397 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.028 ( 213 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 184 hom. )

Consequence

AK9
NM_001145128.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.456
Variant links:
Genes affected
AK9 (HGNC:33814): (adenylate kinase 9) The protein encoded by this gene catalyzes the interconversion of nucleosides, possessing both nucleoside monophosphate and diphosphate kinase activities. The encoded protein uses these interconversions to maintain nucleoside homeostasis. [provided by RefSeq, Jul 2016]
ZBTB24-DT (HGNC:55872): (ZBTB24 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-109497503-A-G is Benign according to our data. Variant chr6-109497503-A-G is described in ClinVar as [Benign]. Clinvar id is 792049.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.456 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0946 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AK9NM_001145128.3 linkuse as main transcriptc.5277T>C p.Tyr1759= synonymous_variant 38/41 ENST00000424296.7
ZBTB24-DTXR_942855.3 linkuse as main transcriptn.401+2935A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AK9ENST00000424296.7 linkuse as main transcriptc.5277T>C p.Tyr1759= synonymous_variant 38/415 NM_001145128.3 P1Q5TCS8-4
ZBTB24-DTENST00000658720.1 linkuse as main transcriptn.1428+2935A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0283
AC:
4300
AN:
152104
Hom.:
214
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0974
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0132
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000265
Gnomad OTH
AF:
0.0230
GnomAD3 exomes
AF:
0.00729
AC:
1825
AN:
250494
Hom.:
89
AF XY:
0.00502
AC XY:
680
AN XY:
135520
show subpopulations
Gnomad AFR exome
AF:
0.101
Gnomad AMR exome
AF:
0.00453
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000164
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000194
Gnomad OTH exome
AF:
0.00410
GnomAD4 exome
AF:
0.00286
AC:
4171
AN:
1455950
Hom.:
184
Cov.:
31
AF XY:
0.00244
AC XY:
1769
AN XY:
724732
show subpopulations
Gnomad4 AFR exome
AF:
0.103
Gnomad4 AMR exome
AF:
0.00569
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000221
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000822
Gnomad4 OTH exome
AF:
0.00605
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0283
AC:
4301
AN:
152222
Hom.:
213
Cov.:
32
AF XY:
0.0269
AC XY:
1999
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0971
Gnomad4 AMR
AF:
0.0132
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000265
Gnomad4 OTH
AF:
0.0228
Alfa
AF:
0.0139
Hom.:
50
Bravo
AF:
0.0333
Asia WGS
AF:
0.00491
AC:
18
AN:
3478
EpiCase
AF:
0.000327
EpiControl
AF:
0.000237

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
Cadd
Benign
4.0
Dann
Benign
0.75

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: rs9487128; hg19: chr6-109818706; COSMIC: COSV101414001; API