rs6601899

Positions:

• chr10-5076130-A-C

Variant summary

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

The XR_001747341.2(LOC107984198):​n.717-1770A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,164 control chromosomes in the GnomAD database, including 58,012 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 0.87 (58012 hom., cov: 31)
• Consequence: LOC107984198 XR_001747341.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

LOC107984198 (HGNC:):

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984198	XR_001747341.2	n.717-1770A>C		intron_variant, non_coding_transcript_variant
AKR1C3	NM_001253908.2	c.85-20280A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1C3	ENST00000439082.7	c.85-20280A>C		intron_variant		5		A1
AKR1C3	ENST00000602997.5	c.-63-1770A>C		intron_variant		3
AKR1C3	ENST00000470862.6	n.261-1740A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132470 AN: 152046 Hom.: 57952 Cov.: 31

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.871 AC: 132589 AN: 152164 Hom.: 58012 Cov.: 31 AF XY: 0.870 AC XY: 64742 AN XY: 74382

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.893

Alfa AF: 0.857 Hom.: 9691

Bravo AF: 0.877

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6601899; hg19: chr10-5118322;