Variant 6-109499227-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001145128.3(AK9):c.4863C>T(p.Cys1621=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00475 in 1,517,468 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0030 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 35 hom. )

Consequence

AK9
NM_001145128.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.18

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]

AK9 links:

ZBTB24-DT (HGNC:55872): (ZBTB24 divergent transcript)

ZBTB24-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 6-109499227-G-A is Benign according to our data. Variant chr6-109499227-G-A is described in ClinVar as [Benign]. Clinvar id is 2656829.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 35 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AK9	NM_001145128.3 linkuse as main transcript	c.4863C>T	p.Cys1621=	synonymous_variant	36/41	ENST00000424296.7	NP_001138600.2
ZBTB24-DT	XR_942855.3 linkuse as main transcript	n.402-2377G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AK9	ENST00000424296.7 linkuse as main transcript	c.4863C>T	p.Cys1621=	synonymous_variant	36/41	5	NM_001145128.3	ENSP00000410186	P1	Q5TCS8-4
ZBTB24-DT	ENST00000658720.1 linkuse as main transcript	n.1428+4659G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00300

AC:

456

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000845

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000916

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0147

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00475

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00383

AC:

769

AN:

200876

Hom.:

AF XY:

0.00444

AC XY:

487

AN XY:

109766

show subpopulations

Gnomad AFR exome

AF:

0.000910

Gnomad AMR exome

AF:

0.00114

Gnomad ASJ exome

AF:

0.00327

Gnomad EAS exome

AF:

0.000137

Gnomad SAS exome

AF:

0.0125

Gnomad FIN exome

AF:

0.000347

Gnomad NFE exome

AF:

0.00423

Gnomad OTH exome

AF:

0.00398

GnomAD4 exome

AF:

0.00495

AC:

6754

AN:

1365172

Hom.:

Cov.:

AF XY:

0.00515

AC XY:

3456

AN XY:

671560

show subpopulations

Gnomad4 AFR exome

AF:

0.000468

Gnomad4 AMR exome

AF:

0.000887

Gnomad4 ASJ exome

AF:

0.00248

Gnomad4 EAS exome

AF:

0.000163

Gnomad4 SAS exome

AF:

0.0127

Gnomad4 FIN exome

AF:

0.000427

Gnomad4 NFE exome

AF:

0.00518

Gnomad4 OTH exome

AF:

0.00340

GnomAD4 genome

AF:

0.00299

AC:

456

AN:

152296

Hom.:

Cov.:

AF XY:

0.00301

AC XY:

224

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.000842

Gnomad4 AMR

AF:

0.000915

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0147

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00475

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00348

Hom.:

Bravo

AF:

0.00241

Asia WGS

AF:

0.00404

AC:

AN:

3478

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

AK9: BS1, BS2; ZBTB24-DT: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.21

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.21

Position offset: -29

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over