chr10-5090396-C-T

Variant names:

• chr10-5090396-C-T
• rs17134288
• NM_001253908.2:c.85-6014C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001253908.2(AKR1C3):​c.85-6014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,880 control chromosomes in the GnomAD database, including 8,079 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 0.31 (8079 hom., cov: 31)
• Consequence: AKR1C3 NM_001253908.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKR1C3	NM_001253908.2	c.85-6014C>T		intron_variant	Intron 1 of 8		NP_001240837.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKR1C3	ENST00000439082.7	c.85-6014C>T		intron_variant	Intron 1 of 8	5		ENSP00000401327.3
AKR1C3	ENST00000605149.5	c.16-6014C>T		intron_variant	Intron 1 of 8	2		ENSP00000474882.1
AKR1C3	ENST00000602997.5	c.16-6014C>T		intron_variant	Intron 2 of 5	3		ENSP00000474188.1

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47767 AN: 151762 Hom.: 8075 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.315 AC: 47802 AN: 151880 Hom.: 8079 Cov.: 31 AF XY: 0.313 AC XY: 23220 AN XY: 74230

African (AFR) AF: 0.301 AC: 12435 AN: 41356

American (AMR) AF: 0.252 AC: 3840 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5176

South Asian (SAS) AF: 0.182 AC: 875 AN: 4810

European-Finnish (FIN) AF: 0.404 AC: 4275 AN: 10570

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24594 AN: 67936

Other (OTH) AF: 0.272 AC: 573 AN: 2106

Alfa AF: 0.337 Hom.: 1150

Bravo AF: 0.300

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.1
DANN	Benign	0.88
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17134288; hg19: chr10-5132588; COSMIC: COSV65911060; COSMIC: COSV65911060;