ENST00000305623.12:n.412C>T

Variant names:

• chr10-5283724-G-A
• rs9423590
• ENST00000305623.12:n.412C>T

Variant summary

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

The ENST00000305623.12(AKR1C7P):​n.412C>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: AKR1C7P ENST00000305623.12 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 6 publications found

Genes affected

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

ENSG00000291045 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AKR1C7P		n.5283724G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKR1C7P	ENST00000305623.12	n.412C>T		non_coding_transcript_exon_variant	Exon 4 of 8	6
ENSG00000291045	ENST00000432689.2	n.262C>T		non_coding_transcript_exon_variant	Exon 3 of 6	3
ENSG00000291045	ENST00000701390.2	n.355C>T		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AF: 0.0286 AC: 2 AN: 70

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.163 AC: 14 AN: 86

European-Finnish (FIN) AF: 0.234 AC: 1193 AN: 5090

Middle Eastern (MID) AF: 0.127 AC: 207 AN: 1624

European-Non Finnish (NFE) AF: 0.222 AC: 32 AN: 144

Other (OTH) AF: 0.129 AC: 27 AN: 210

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

African (AFR) AF: 0.0444 AC: 1842 AN: 41492

American (AMR) AF: 0.148 AC: 2271 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5174

South Asian (SAS) AF: 0.0849 AC: 409 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1918 AN: 10556

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13501 AN: 67966

Other (OTH) AF: 0.141 AC: 298 AN: 2110

Alfa AF: 0.160 Hom.: 1253

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9423590; hg19: chr10-5325687;