rs28942669

chr10-5092812-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001253908.2(AKR1C3):c.85-3598C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,044 control chromosomes in the GnomAD database, including 350 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 0.063 (350 hom., cov: 32)
• Consequence: AKR1C3 NM_001253908.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

AKR1C3 (HGNC:386): (aldo-keto reductase family 1 member C3) This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. These enzymes catalyze the conversion of aldehydes and ketones to their corresponding alcohols by utilizing NADH and/or NADPH as cofactors. The enzymes display overlapping but distinct substrate specificity. This enzyme catalyzes the reduction of prostaglandin (PG) D2, PGH2 and phenanthrenequinone (PQ), and the oxidation of 9alpha,11beta-PGF2 to PGD2. It may play an important role in the pathogenesis of allergic diseases such as asthma, and may also have a role in controlling cell growth and/or differentiation. This gene shares high sequence identity with three other gene members and is clustered with those three genes at chromosome 10p15-p14. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKR1C3	NM_001253908.2	c.85-3598C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1C3	ENST00000439082.7	c.85-3598C>T		intron_variant		5		A1
AKR1C3	ENST00000602997.5	c.16-3598C>T		intron_variant		3
AKR1C3	ENST00000605149.5	c.16-3598C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9519 AN: 151926 Hom.: 349 Cov.: 32

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0692

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0627 AC: 9528 AN: 152044 Hom.: 350 Cov.: 32 AF XY: 0.0620 AC XY: 4606 AN XY: 74326

Gnomad4 AFR AF: 0.0587

Gnomad4 AMR AF: 0.0582

Gnomad4 ASJ AF: 0.0551

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0195

Gnomad4 FIN AF: 0.0931

Gnomad4 NFE AF: 0.0692

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0730 Hom.: 62

Bravo AF: 0.0609

Asia WGS AF: 0.0130 AC: 48 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	2.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28942669; hg19: chr10-5135004;