chr10-5095654-A-G

Variant names:

• chr10-5095654-A-G
• rs17396032
• NM_003739.6:c.85-756A>G

Variant summary

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

The NM_003739.6(AKR1C3):​c.85-756A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0411 in 152,212 control chromosomes in the GnomAD database, including 193 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 0.041 (193 hom., cov: 32)
• Consequence: AKR1C3 NM_003739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003739.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKR1C3	NM_003739.6	MANE Select	c.85-756A>G		intron	N/A	NP_003730.4
	AKR1C3	NM_001253908.2		c.85-756A>G		intron	N/A	NP_001240837.1
	AKR1C3	NM_001253909.2		c.85-756A>G		intron	N/A	NP_001240838.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKR1C3	ENST00000380554.5	TSL:1 MANE Select	c.85-756A>G		intron	N/A	ENSP00000369927.3
	AKR1C3	ENST00000480697.6	TSL:1	n.116-756A>G		intron	N/A
	AKR1C3	ENST00000605322.1	TSL:1	n.112-756A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0411 AC: 6258 AN: 152094 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0232

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.00893

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0259

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

GnomAD4 genome AF: 0.0411 AC: 6258 AN: 152212 Hom.: 193 Cov.: 32 AF XY: 0.0407 AC XY: 3031 AN XY: 74430

African (AFR) AF: 0.0110 AC: 458 AN: 41540

American (AMR) AF: 0.0232 AC: 354 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.00873 AC: 42 AN: 4812

European-Finnish (FIN) AF: 0.0719 AC: 763 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4426 AN: 67992

Other (OTH) AF: 0.0256 AC: 54 AN: 2110

Alfa AF: 0.0291 Hom.: 20

Bravo AF: 0.0367

Asia WGS AF: 0.00607 AC: 22 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.91
PhyloP100		0.030
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17396032; hg19: chr10-5137846;