rs4266965

chr10-4873586-C-Achr10-4873586-C-Gchr10-4873586-C-T

Variant summary

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

The NR_026743.1(AKR1C6P):n.1126-1648G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,804 control chromosomes in the GnomAD database, including 35,718 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 0.67 (35718 hom., cov: 30)
• Consequence: AKR1C6P NR_026743.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

Genes affected

AKR1C6P (HGNC:44680): (aldo-keto reductase family 1 member C6, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKR1C6P	NR_026743.1	n.1126-1648G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1C6P	ENST00000432950.1	n.946-1648G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.672 AC: 101875 AN: 151686 Hom.: 35696 Cov.: 30

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.674

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.672 AC: 101938 AN: 151804 Hom.: 35718 Cov.: 30 AF XY: 0.677 AC XY: 50183 AN XY: 74172

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.670

Alfa AF: 0.726 Hom.: 18584

Bravo AF: 0.660

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.0
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4266965; hg19: chr10-4915778;