rs7092182

Positions:

• chr10-4885460-G-A
• chr10-4885460-G-C
• chr10-4885460-G-T

Variant summary

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

The ENST00000432950.1(AKR1C6P):​n.516C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 756,294 control chromosomes in the GnomAD database, including 312,292 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 0.84 (55534 hom., cov: 30)
  • Exomes 𝑓: 0.92 (256758 hom.)
• Consequence: AKR1C6P ENST00000432950.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

Genes affected

AKR1C6P (HGNC:44680): (aldo-keto reductase family 1 member C6, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKR1C6P	NR_026743.1	n.653-367C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1C6P	ENST00000432950.1	n.516C>T		non_coding_transcript_exon_variant	5/9

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128155 AN: 151910 Hom.: 55514 Cov.: 30

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.872

GnomAD4 exome AF: 0.920 AC: 555807 AN: 604266 Hom.: 256758 Cov.: 0 AF XY: 0.920 AC XY: 303767 AN XY: 330146

Gnomad4 AFR exome AF: 0.616

Gnomad4 AMR exome AF: 0.953

Gnomad4 ASJ exome AF: 0.932

Gnomad4 EAS exome AF: 0.929

Gnomad4 SAS exome AF: 0.883

Gnomad4 FIN exome AF: 0.890

Gnomad4 NFE exome AF: 0.943

Gnomad4 OTH exome AF: 0.905

GnomAD4 genome AF: 0.843 AC: 128223 AN: 152028 Hom.: 55534 Cov.: 30 AF XY: 0.843 AC XY: 62617 AN XY: 74296

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.871

Alfa AF: 0.863 Hom.: 10117

Bravo AF: 0.837

Asia WGS AF: 0.843 AC: 2932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	3.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7092182; hg19: chr10-4927652;