chr10-4873586-C-A

Variant names:

• chr10-4873586-C-A
• rs4266965
• ENST00000432950.1:n.946-1648G>T

Variant summary

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

The NR_026743.1(AKR1C6P):​n.1126-1648G>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 4 publications found

Genes affected

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

ENSG00000304775 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_026743.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKR1C6P	NR_026743.1		n.1126-1648G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKR1C6P	ENST00000432950.1	TSL:6	n.946-1648G>T		intron	N/A
	ENSG00000304775	ENST00000806213.1		n.1022-1648G>T		intron	N/A
	ENSG00000304775	ENST00000806214.1		n.494-1648G>T		intron	N/A

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

African (AFR) AF: 0.452 AC: 18681 AN: 41350

American (AMR) AF: 0.750 AC: 11442 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2137 AN: 3462

East Asian (EAS) AF: 0.872 AC: 4476 AN: 5132

South Asian (SAS) AF: 0.721 AC: 3464 AN: 4802

European-Finnish (FIN) AF: 0.793 AC: 8360 AN: 10540

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51141 AN: 67954

Other (OTH) AF: 0.670 AC: 1410 AN: 2104

Alfa AF: 0.725 Hom.: 20807

Bravo AF: 0.660

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.84
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs4266965; hg19: chr10-4915778;