rs7921327

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-5117261-G-A
• chr10-5117261-G-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
• Publications: 1 publications found

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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

Other links and lift over

dbSNP: rs7921327; hg19: chr10-5159453;