chr10-5119763-A-G

Variant names:

• chr10-5119763-A-G
• rs1937920
• XM_047425162.1:c.*405-2733T>C

Variant summary

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

The XM_047425162.1(AKR1C8):​c.*405-2733T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,084 control chromosomes in the GnomAD database, including 6,407 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 0.28 (6407 hom., cov: 32)
• Consequence: AKR1C8 XM_047425162.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51
• Publications: 14 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42519 AN: 151968 Hom.: 6395 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.280 AC: 42568 AN: 152084 Hom.: 6407 Cov.: 32 AF XY: 0.275 AC XY: 20471 AN XY: 74354

African (AFR) AF: 0.388 AC: 16103 AN: 41478

American (AMR) AF: 0.241 AC: 3681 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5176

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4818

European-Finnish (FIN) AF: 0.223 AC: 2360 AN: 10578

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16107 AN: 67986

Other (OTH) AF: 0.316 AC: 666 AN: 2106

Alfa AF: 0.250 Hom.: 13500

Bravo AF: 0.288

Asia WGS AF: 0.280 AC: 974 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs1937920; hg19: chr10-5161955;