rs7921327

chr10-5117261-G-Achr10-5117261-G-T

Variant summary

Our verdict is Benign. Variant got -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:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
AKR1C8	XM_047425162.1	c.*405-231C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.651

Alfa AF: 0.666 Hom.: 29556

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7921327; hg19: chr10-5159453;