10-4825966-T-G

Position:

• chr10-4825966-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000533295.5(AKR1E2):​c.51+928T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0534 in 152,272 control chromosomes in the GnomAD database, including 257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.053 (257 hom., cov: 34)
• Consequence: AKR1E2 ENST00000533295.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.691

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 10-4825966-T-G is Benign according to our data. Variant chr10-4825966-T-G is described in ClinVar as [Benign]. Clinvar id is 1269322.Status of the report is criteria_provided_single_submitter, 1 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	Protein	UniProt
AKR1E2	XM_011519715.3	c.51+928T>G		intron_variant			XP_011518017.2
AKR1E2	XR_001747220.2	n.66+928T>G		intron_variant
AKR1E2	XR_930518.3	n.66+928T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKR1E2	ENST00000533295.5	c.51+928T>G		intron_variant		3		ENSP00000435436.1
AKR1E2	ENST00000462718.7	n.53-4709T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8130 AN: 152154 Hom.: 257 Cov.: 34

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0310

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0534 AC: 8134 AN: 152272 Hom.: 257 Cov.: 34 AF XY: 0.0523 AC XY: 3891 AN XY: 74458

Gnomad4 AFR AF: 0.0399

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0381

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0811

Gnomad4 NFE AF: 0.0682

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0209 Hom.: 16

Bravo AF: 0.0502

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78832739; hg19: chr10-4868158;