chr10-4830459-GT-G

Position:

• chr10-4830459-GT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001040177.3(AKR1E2):​c.40-207del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 151,076 control chromosomes in the GnomAD database, including 149 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.036 (149 hom., cov: 32)
• Consequence: AKR1E2 NM_001040177.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.616

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-4830459-GT-G is Benign according to our data. Variant chr10-4830459-GT-G is described in ClinVar as [Benign]. Clinvar id is 1302864.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKR1E2	NM_001040177.3	c.40-207del		intron_variant		ENST00000298375.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1E2	ENST00000298375.12	c.40-207del		intron_variant		1	NM_001040177.3	P1

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5395 AN: 150962 Hom.: 149 Cov.: 32

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0223

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0376

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

GnomAD4 genome AF: 0.0357 AC: 5392 AN: 151076 Hom.: 149 Cov.: 32 AF XY: 0.0340 AC XY: 2509 AN XY: 73812

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0223

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0377

Alfa AF: 0.0216 Hom.: 12

Bravo AF: 0.0366

Asia WGS AF: 0.0540 AC: 186 AN: 3476

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

Jul 27, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs3833732; hg19: chr10-4872651;