Variant chr10-4830719-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001040177.3(AKR1E2):c.84C>T(p.Asp28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 1,613,970 control chromosomes in the GnomAD database, including 1,822 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.035 ( 148 hom., cov: 32)

Exomes 𝑓: 0.043 ( 1674 hom. )

Consequence

AKR1E2
NM_001040177.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.08

Variant links:

Genes affected

AKR1E2 (HGNC:23437): (aldo-keto reductase family 1 member E2) The protein encoded by this gene is a member of the aldo-keto reductase superfamily. Members in this family are characterized by their structure (evolutionarily highly conserved TIM barrel) and function (NAD(P)H-dependent oxido-reduction of carbonyl groups). Transcripts of this gene have been reported in specimens of human testis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

AKR1E2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 10-4830719-C-T is Benign according to our data. Variant chr10-4830719-C-T is described in ClinVar as [Benign]. Clinvar id is 1253619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.08 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKR1E2	NM_001040177.3 linkuse as main transcript	c.84C>T	p.Asp28=	synonymous_variant	2/10	ENST00000298375.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1E2	ENST00000298375.12 linkuse as main transcript	c.84C>T	p.Asp28=	synonymous_variant	2/10	1	NM_001040177.3	P1	Q96JD6-1

Frequencies

GnomAD3 genomes

AF:

0.0349

AC:

5313

AN:

152070

Hom.:

148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00985

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0348

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.0218

Gnomad FIN

AF:

0.0161

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0496

Gnomad OTH

AF:

0.0373

GnomAD3 exomes

AF:

0.0401

AC:

10091

AN:

251392

Hom.:

302

AF XY:

0.0397

AC XY:

5400

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.00886

Gnomad AMR exome

AF:

0.0317

Gnomad ASJ exome

AF:

0.0164

Gnomad EAS exome

AF:

0.120

Gnomad SAS exome

AF:

0.0170

Gnomad FIN exome

AF:

0.0162

Gnomad NFE exome

AF:

0.0475

Gnomad OTH exome

AF:

0.0340

GnomAD4 exome

AF:

0.0435

AC:

63518

AN:

1461782

Hom.:

1674

Cov.:

AF XY:

0.0430

AC XY:

31237

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.00714

Gnomad4 AMR exome

AF:

0.0316

Gnomad4 ASJ exome

AF:

0.0155

Gnomad4 EAS exome

AF:

0.124

Gnomad4 SAS exome

AF:

0.0171

Gnomad4 FIN exome

AF:

0.0185

Gnomad4 NFE exome

AF:

0.0466

Gnomad4 OTH exome

AF:

0.0366

GnomAD4 genome

AF:

0.0349

AC:

5310

AN:

152188

Hom.:

148

Cov.:

AF XY:

0.0333

AC XY:

2475

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.00983

Gnomad4 AMR

AF:

0.0347

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.0218

Gnomad4 FIN

AF:

0.0161

Gnomad4 NFE

AF:

0.0496

Gnomad4 OTH

AF:

0.0374

Alfa

AF:

0.0368

Hom.:

Bravo

AF:

0.0361

Asia WGS

AF:

0.0540

AC:

187

AN:

3478

EpiCase

AF:

0.0459

EpiControl

AF:

0.0484

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 21, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.7

DANN

Benign

0.30

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

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