chr10-5208400-A-T

Position:

• chr10-5208400-A-T

Variant summary

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

The NM_001818.5(AKR1C4):​c.570+2003A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,382 control chromosomes in the GnomAD database, including 51,619 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 0.80 (51619 hom., cov: 33)
• Consequence: AKR1C4 NM_001818.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

Genes affected

AKR1C4 (HGNC:387): (aldo-keto reductase family 1 member C4) This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. These enzymes catalyze the conversion of aldehydes and ketones to their corresponding alcohols by utilizing NADH and/or NADPH as cofactors. The enzymes display overlapping but distinct substrate specificity. This enzyme catalyzes the bioreduction of chlordecone, a toxic organochlorine pesticide, to chlordecone alcohol in liver. This gene shares high sequence identity with three other gene members and is clustered with those three genes at chromosome 10p15-p14. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AKR1C4	NM_001818.5	c.570+2003A>T		intron_variant		ENST00000263126.3	NP_001809.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKR1C4	ENST00000263126.3	c.570+2003A>T		intron_variant		1	NM_001818.5	ENSP00000263126	P1
AKR1C4	ENST00000380448.5	c.570+2003A>T		intron_variant		5		ENSP00000369814	P1

Frequencies

GnomAD3 genomes AF: 0.805 AC: 121704 AN: 151264 Hom.: 51596 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.804 AC: 121771 AN: 151382 Hom.: 51619 Cov.: 33 AF XY: 0.811 AC XY: 60034 AN XY: 73988

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.818

Alfa AF: 0.811 Hom.: 3206

Bravo AF: 0.790

Asia WGS AF: 0.902 AC: 3129 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.0
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1413624; hg19: chr10-5250363;