rs9423590

Positions:

• chr10-5283724-G-A
• chr10-5283724-G-T

Variant summary

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

The ENST00000432689.2(ENSG00000291045):​n.262C>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 0.141 in 159,322 control chromosomes in the GnomAD database, including 2,033 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 0.14 (1876 hom., cov: 32)
  • Exomes 𝑓: 0.20 (157 hom.)
• Consequence: ENSG00000291045 ENST00000432689.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

AKR1C7P (HGNC:44681): (aldo-keto reductase family 1 member C7, pseudogene)

ENSG00000291045 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AKR1C7P		n.5283724G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKR1C7P	ENST00000305623.12	n.412C>T		non_coding_transcript_exon_variant	4/8	6
ENSG00000291045	ENST00000432689.2	n.262C>T		non_coding_transcript_exon_variant	3/6	3
ENSG00000291045	ENST00000701390.1	n.318C>T		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20919 AN: 151972 Hom.: 1875 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.204 AC: 1477 AN: 7232 Hom.: 157 Cov.: 0 AF XY: 0.199 AC XY: 717 AN XY: 3594

Gnomad4 AFR exome AF: 0.0286

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.250

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.234

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.129

GnomAD4 genome AF: 0.138 AC: 20918 AN: 152090 Hom.: 1876 Cov.: 32 AF XY: 0.135 AC XY: 10060 AN XY: 74344

Gnomad4 AFR AF: 0.0444

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0849

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.141

Alfa AF: 0.157 Hom.: 1118

Bravo AF: 0.132

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
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: rs9423590; hg19: chr10-5325687;