10-4885460-G-A

Variant names:

• chr10-4885460-G-A
• rs7092182
• ENST00000432950.1:n.516C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ENSG00000304775 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AKR1C6P	NR_026743.1	n.653-367C>T		intron_variant	Intron 6 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKR1C6P	ENST00000432950.1	n.516C>T		non_coding_transcript_exon_variant	Exon 5 of 9	6
ENSG00000304775	ENST00000806213.1	n.662+1878C>T		intron_variant	Intron 5 of 8
ENSG00000304775	ENST00000806214.1	n.135-7896C>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.616 AC: 10531 AN: 17108

American (AMR) AF: 0.953 AC: 40804 AN: 42838

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 18603 AN: 19960

East Asian (EAS) AF: 0.929 AC: 32779 AN: 35288

South Asian (SAS) AF: 0.883 AC: 61179 AN: 69256

European-Finnish (FIN) AF: 0.890 AC: 44394 AN: 49894

Middle Eastern (MID) AF: 0.917 AC: 2822 AN: 3076

European-Non Finnish (NFE) AF: 0.943 AC: 316516 AN: 335720

Other (OTH) AF: 0.905 AC: 28179 AN: 31126

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

African (AFR) AF: 0.621 AC: 25691 AN: 41396

American (AMR) AF: 0.918 AC: 14044 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3216 AN: 3468

East Asian (EAS) AF: 0.908 AC: 4655 AN: 5128

South Asian (SAS) AF: 0.877 AC: 4225 AN: 4820

European-Finnish (FIN) AF: 0.893 AC: 9460 AN: 10590

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64026 AN: 68008

Other (OTH) AF: 0.871 AC: 1842 AN: 2114

Alfa AF: 0.857 Hom.: 10292

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7092182; hg19: chr10-4927652;