10-5106261-C-T

Variant summary

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

The NM_003739.6(AKR1C3):c.929+584C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,070 control chromosomes in the GnomAD database, including 4,001 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 0.20 (4001 hom., cov: 32)
• Consequence: AKR1C3 NM_003739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKR1C3	NM_003739.6	c.929+584C>T		intron_variant		ENST00000380554.5
AKR1C3	NM_001253908.2	c.929+584C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1C3	ENST00000380554.5	c.929+584C>T		intron_variant		1	NM_003739.6	P4
AKR1C3	ENST00000439082.7	c.929+584C>T		intron_variant		5		A1
AKR1C3	ENST00000605149.5	c.860+584C>T		intron_variant		2
AKR1C3	ENST00000603484.1	n.403+584C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31014 AN: 151952 Hom.: 4001 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.204 AC: 31033 AN: 152070 Hom.: 4001 Cov.: 32 AF XY: 0.209 AC XY: 15529 AN XY: 74336

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.230

Alfa AF: 0.199 Hom.: 478

Bravo AF: 0.214

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.76
Dann	Benign	0.40

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: rs4641368; hg19: chr10-5148453;