10-5284883-C-T

Position:

• chr10-5284883-C-T

Variant summary

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

The ENST00000432689.2(ENSG00000291045):​n.130G>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: ENSG00000291045 ENST00000432689.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

AKR1C7P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
AKR1C7P		n.5284883C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKR1C7P	ENST00000305623.12	n.280G>A		non_coding_transcript_exon_variant	3/8	6
ENSG00000291045	ENST00000432689.2	n.130G>A		non_coding_transcript_exon_variant	2/6	3

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

Gnomad4 AFR exome AF: 0.258

Gnomad4 AMR exome AF: 0.325

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.100

Gnomad4 SAS exome AF: 0.272

Gnomad4 FIN exome AF: 0.436

Gnomad4 NFE exome AF: 0.420

Gnomad4 OTH exome AF: 0.301

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

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.286

Alfa AF: 0.351 Hom.: 16539

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7906894; hg19: chr10-5326846;