Variant chr1-45570088-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The 1-45570088-A-T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 917,850 control chromosomes in the GnomAD database, including 107,523 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 16877 hom., cov: 32)

Exomes 𝑓: 0.49 ( 90646 hom. )

Consequence

AKR1A1
ENST00000351829.9 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.519

Variant links:

Genes affected

AKR1A1 (HGNC:380): (aldo-keto reductase family 1 member A1) This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. This member, also known as aldehyde reductase, is involved in the reduction of biogenic and xenobiotic aldehydes and is present in virtually every tissue. Multiple alternatively spliced transcript variants of this gene exist, all encoding the same protein. [provided by RefSeq, Jan 2011]

AKR1A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AKR1A1	NM_153326.3 linkuse as main transcript			downstream_gene_variant		ENST00000351829.9	NP_697021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKR1A1	ENST00000351829.9 linkuse as main transcript			downstream_gene_variant		1	NM_153326.3	ENSP00000312606	P1

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71320

AN:

151932

Hom.:

16892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.426

Gnomad AMI

AF:

0.487

Gnomad AMR

AF:

0.513

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.624

Gnomad SAS

AF:

0.507

Gnomad FIN

AF:

0.483

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.462

GnomAD4 exome

AF:

0.485

AC:

371629

AN:

765800

Hom.:

90646

Cov.:

AF XY:

0.485

AC XY:

192535

AN XY:

396888

show subpopulations

Gnomad4 AFR exome

AF:

0.423

Gnomad4 AMR exome

AF:

0.558

Gnomad4 ASJ exome

AF:

0.503

Gnomad4 EAS exome

AF:

0.649

Gnomad4 SAS exome

AF:

0.498

Gnomad4 FIN exome

AF:

0.487

Gnomad4 NFE exome

AF:

0.469

Gnomad4 OTH exome

AF:

0.486

GnomAD4 genome

AF:

0.469

AC:

71304

AN:

152050

Hom.:

16877

Cov.:

AF XY:

0.472

AC XY:

35059

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.425

Gnomad4 AMR

AF:

0.513

Gnomad4 ASJ

AF:

0.507

Gnomad4 EAS

AF:

0.624

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.483

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.456

Alfa

AF:

0.312

Hom.:

762

Bravo

AF:

0.468

Asia WGS

AF:

0.537

AC:

1865

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.68

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over