ENST00000305623.12:n.280G>A

Variant names:

• chr10-5284883-C-T
• rs7906894
• ENST00000305623.12:n.280G>A

Variant summary

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

The ENST00000305623.12(AKR1C7P):​n.280G>A 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 0.325 in 156,270 control chromosomes in the GnomAD database, including 8,511 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 0.32 (8263 hom., cov: 32)
  • Exomes 𝑓: 0.33 (248 hom.)
• Consequence: AKR1C7P ENST00000305623.12 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 5 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000305623.12. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKR1C7P	ENST00000305623.12	TSL:6	n.280G>A		non_coding_transcript_exon	Exon 3 of 8
	ENSG00000291045	ENST00000432689.2	TSL:3	n.130G>A		non_coding_transcript_exon	Exon 2 of 6
	ENSG00000291045	ENST00000744973.1		n.359G>A		non_coding_transcript_exon	Exon 3 of 9

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49335 AN: 151940 Hom.: 8257 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.288

GnomAD4 exome AF: 0.333 AC: 1401 AN: 4212 Hom.: 248 Cov.: 0 AF XY: 0.327 AC XY: 723 AN XY: 2208

African (AFR) AF: 0.258 AC: 17 AN: 66

American (AMR) AF: 0.325 AC: 13 AN: 40

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 6 AN: 38

East Asian (EAS) AF: 0.100 AC: 1 AN: 10

South Asian (SAS) AF: 0.272 AC: 37 AN: 136

European-Finnish (FIN) AF: 0.436 AC: 616 AN: 1414

Middle Eastern (MID) AF: 0.222 AC: 352 AN: 1586

European-Non Finnish (NFE) AF: 0.420 AC: 288 AN: 686

Other (OTH) AF: 0.301 AC: 71 AN: 236

GnomAD4 genome AF: 0.325 AC: 49378 AN: 152058 Hom.: 8263 Cov.: 32 AF XY: 0.322 AC XY: 23908 AN XY: 74326

African (AFR) AF: 0.290 AC: 12020 AN: 41478

American (AMR) AF: 0.301 AC: 4603 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3472

East Asian (EAS) AF: 0.120 AC: 620 AN: 5172

South Asian (SAS) AF: 0.278 AC: 1344 AN: 4826

European-Finnish (FIN) AF: 0.349 AC: 3688 AN: 10566

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25237 AN: 67942

Other (OTH) AF: 0.286 AC: 606 AN: 2116

Alfa AF: 0.349 Hom.: 34741

Bravo AF: 0.317

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.45
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7906894; hg19: chr10-5326846;