Variant chr10-4826373-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001040177.3(AKR1E2):c.39+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 1,233,506 control chromosomes in the GnomAD database, including 2,770 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 254 hom., cov: 32)

Exomes 𝑓: 0.066 ( 2516 hom. )

Consequence

AKR1E2
NM_001040177.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.82

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 10-4826373-T-C is Benign according to our data. Variant chr10-4826373-T-C is described in ClinVar as [Benign]. Clinvar id is 1246064.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0666 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.39+10T>C		intron_variant		ENST00000298375.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1E2	ENST00000298375.12 linkuse as main transcript	c.39+10T>C		intron_variant		1	NM_001040177.3	P1	Q96JD6-1

Frequencies

GnomAD3 genomes

AF:

0.0516

AC:

7838

AN:

151858

Hom.:

254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0328

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.0307

Gnomad ASJ

AF:

0.0397

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.0243

Gnomad FIN

AF:

0.0813

Gnomad MID

AF:

0.0478

Gnomad NFE

AF:

0.0683

Gnomad OTH

AF:

0.0450

GnomAD3 exomes

AF:

0.0553

AC:

181

AN:

3274

Hom.:

AF XY:

0.0521

AC XY:

AN XY:

1784

show subpopulations

Gnomad AFR exome

AF:

0.0307

Gnomad AMR exome

AF:

0.0357

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0238

Gnomad FIN exome

AF:

0.0699

Gnomad NFE exome

AF:

0.0493

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0661

AC:

71512

AN:

1081540

Hom.:

2516

Cov.:

AF XY:

0.0658

AC XY:

33625

AN XY:

510908

show subpopulations

Gnomad4 AFR exome

AF:

0.0377

Gnomad4 AMR exome

AF:

0.0287

Gnomad4 ASJ exome

AF:

0.0400

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0261

Gnomad4 FIN exome

AF:

0.0883

Gnomad4 NFE exome

AF:

0.0704

Gnomad4 OTH exome

AF:

0.0554

GnomAD4 genome

AF:

0.0516

AC:

7842

AN:

151966

Hom.:

254

Cov.:

AF XY:

0.0506

AC XY:

3759

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.0328

Gnomad4 AMR

AF:

0.0307

Gnomad4 ASJ

AF:

0.0397

Gnomad4 EAS

AF:

0.000195

Gnomad4 SAS

AF:

0.0243

Gnomad4 FIN

AF:

0.0813

Gnomad4 NFE

AF:

0.0683

Gnomad4 OTH

AF:

0.0445

Alfa

AF:

0.0596

Hom.:

Bravo

AF:

0.0482

Asia WGS

AF:

0.0140

AC:

AN:

3470

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	Sep 05, 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

-0.82

CADD

Benign

1.9

DANN

Benign

0.19

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