10-5117261-G-A

Variant names:

• chr10-5117261-G-A
• rs7921327
• XM_047425162.1:c.*405-231C>T

Variant summary

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

The XM_047425162.1(AKR1C8):​c.*405-231C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,968 control chromosomes in the GnomAD database, including 32,260 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 0.64 (32260 hom., cov: 31)
• Consequence: AKR1C8 XM_047425162.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

AKR1C8 (HGNC:23469): (aldo-keto reductase family 1 member C8) Predicted to enable D-threo-aldose 1-dehydrogenase activity; aldo-keto reductase (NADP) activity; and estradiol 17-beta-dehydrogenase activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKR1C8	XM_047425162.1	c.*405-231C>T		intron_variant	Intron 12 of 13		XP_047281118.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97613 AN: 151850 Hom.: 32215 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.643 AC: 97710 AN: 151968 Hom.: 32260 Cov.: 31 AF XY: 0.637 AC XY: 47326 AN XY: 74264

African (AFR) AF: 0.697 AC: 28901 AN: 41442

American (AMR) AF: 0.547 AC: 8352 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1930 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1253 AN: 5142

South Asian (SAS) AF: 0.412 AC: 1980 AN: 4808

European-Finnish (FIN) AF: 0.723 AC: 7642 AN: 10572

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45356 AN: 67954

Other (OTH) AF: 0.651 AC: 1374 AN: 2110

Alfa AF: 0.652 Hom.: 81014

Bravo AF: 0.633

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		0.064

Splicing

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

Publications

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Other links and lift over

dbSNP: rs7921327; hg19: chr10-5159453;