Genetic Variant AKR1A1:c.*278T>C (chr1-45567302-T-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000471651.1(AKR1A1):c.*278T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 368,810 control chromosomes in the GnomAD database, including 45,378 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 0.50 ( 18909 hom., cov: 32)

Exomes 𝑓: 0.49 ( 26469 hom. )

Consequence

AKR1A1
ENST00000471651.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

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 -8 ACMG points.

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 rank	MANE	Protein	UniProt
AKR1A1	NM_153326.3 link	c.356+282T>C		intron_variant	Intron 4 of 8	ENST00000351829.9	NP_697021.1	P14550V9HWI0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKR1A1	ENST00000351829.9 link	c.356+282T>C		intron_variant	Intron 4 of 8	1	NM_153326.3	ENSP00000312606.4		P14550
AKR1A1	ENST00000481885.5 link	c.356+282T>C		intron_variant	Intron 4 of 4	3		ENSP00000476978.1		V9GYP9

Frequencies

GnomAD3 genomes

AF:

0.498

AC:

75578

AN:

151828

Hom.:

18920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.524

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.625

Gnomad SAS

AF:

0.504

Gnomad FIN

AF:

0.483

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.469

Gnomad OTH

AF:

0.477

GnomAD4 exome

AF:

0.488

AC:

105819

AN:

216864

Hom.:

26469

Cov.:

AF XY:

0.488

AC XY:

54504

AN XY:

111576

show subpopulations

Gnomad4 AFR exome

AF:

0.511

Gnomad4 AMR exome

AF:

0.533

Gnomad4 ASJ exome

AF:

0.496

Gnomad4 EAS exome

AF:

0.658

Gnomad4 SAS exome

AF:

0.483

Gnomad4 FIN exome

AF:

0.485

Gnomad4 NFE exome

AF:

0.465

Gnomad4 OTH exome

AF:

0.484

GnomAD4 genome

AF:

0.497

AC:

75562

AN:

151946

Hom.:

18909

Cov.:

AF XY:

0.500

AC XY:

37112

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.523

Gnomad4 AMR

AF:

0.524

Gnomad4 ASJ

AF:

0.505

Gnomad4 EAS

AF:

0.624

Gnomad4 SAS

AF:

0.503

Gnomad4 FIN

AF:

0.483

Gnomad4 NFE

AF:

0.469

Gnomad4 OTH

AF:

0.471

Alfa

AF:

0.475

Hom.:

22967

Bravo

AF:

0.500

Asia WGS

AF:

0.546

AC:

1895

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.22

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.22

Position offset: -14

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