rs3930965

Variant names:

• chr10-4971951-G-A
• rs3930965
• NM_001353.6:c.571-250G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-4971951-G-A
• chr10-4971951-G-C
• chr10-4971951-G-T

Variant summary

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

The NM_001353.6(AKR1C1):​c.571-250G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00429 in 140,428 control chromosomes in the GnomAD database, including 11 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 0.0043 (11 hom., cov: 25)
• Consequence: AKR1C1 NM_001353.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 1 publications found

Genes affected

AKR1C1 (HGNC:384): (aldo-keto reductase family 1 member C1) 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 reaction of progesterone to the inactive form 20-alpha-hydroxy-progesterone. 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]

LOC124902365 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKR1C1	NM_001353.6	c.571-250G>A		intron_variant	Intron 5 of 8	ENST00000380872.9	NP_001344.2
LOC124902365	XR_007062038.1	n.342C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKR1C1	ENST00000380872.9	c.571-250G>A		intron_variant	Intron 5 of 8	1	NM_001353.6	ENSP00000370254.4
AKR1C1	ENST00000442997.5	c.469-250G>A		intron_variant	Intron 5 of 6	3		ENSP00000416415.1
AKR1C1	ENST00000477661.1	n.2028-250G>A		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.00430 AC: 603 AN: 140318 Hom.: 11 Cov.: 25

Gnomad AFR AF: 0.000238

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000578

Gnomad ASJ AF: 0.00242

Gnomad EAS AF: 0.0825

Gnomad SAS AF: 0.00779

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000701

Gnomad OTH AF: 0.00268

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

GnomAD4 genome AF: 0.00429 AC: 602 AN: 140428 Hom.: 11 Cov.: 25 AF XY: 0.00511 AC XY: 347 AN XY: 67972

African (AFR) AF: 0.000237 AC: 9 AN: 37916

American (AMR) AF: 0.000577 AC: 8 AN: 13862

Ashkenazi Jewish (ASJ) AF: 0.00242 AC: 8 AN: 3306

East Asian (EAS) AF: 0.0825 AC: 384 AN: 4652

South Asian (SAS) AF: 0.00779 AC: 32 AN: 4108

European-Finnish (FIN) AF: 0.0119 AC: 111 AN: 9324

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.000701 AC: 45 AN: 64230

Other (OTH) AF: 0.00265 AC: 5 AN: 1886

Alfa AF: 0.000597 Hom.: 208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.96
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs3930965; hg19: chr10-5014143;