rs7906894

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKR1C7P		n.5284883C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKR1C7P	ENST00000305623.12	n.280G>A		non_coding_transcript_exon_variant	Exon 3 of 8	6
ENSG00000291045	ENST00000432689.2	n.130G>A		non_coding_transcript_exon_variant	Exon 2 of 6	3
ENSG00000291045	ENST00000744973.1	n.359G>A		non_coding_transcript_exon_variant	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 v4.3

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;