rs10114038

Variant names:

• chr9-124565484-A-G
• rs10114038
• NM_033334.4:c.143-10914T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-124565484-A-G
• chr9-124565484-A-T

Variant summary

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

The ENST00000487099.7(NR6A1):​c.143-10914T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 152,214 control chromosomes in the GnomAD database, including 514 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 0.054 (514 hom., cov: 32)
• Consequence: NR6A1 ENST00000487099.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.974
• Publications: 1 publications found

Genes affected

NR6A1 (HGNC:7985): (nuclear receptor subfamily 6 group A member 1) This gene encodes an orphan nuclear receptor which is a member of the nuclear hormone receptor family. Its expression pattern suggests that it may be involved in neurogenesis and germ cell development. The protein can homodimerize and bind DNA, but in vivo targets have not been identified. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487099.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR6A1	NM_033334.4	MANE Select	c.143-10914T>C		intron	N/A	NP_201591.2
	NR6A1	NM_001410996.1		c.143-10914T>C		intron	N/A	NP_001397925.1
	NR6A1	NM_001278546.2		c.143-10926T>C		intron	N/A	NP_001265475.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR6A1	ENST00000487099.7	TSL:1 MANE Select	c.143-10914T>C		intron	N/A	ENSP00000420267.1
	NR6A1	ENST00000373584.7	TSL:1	c.143-10926T>C		intron	N/A	ENSP00000362686.3
	NR6A1	ENST00000416460.6	TSL:1	c.143-10926T>C		intron	N/A	ENSP00000413701.2

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8200 AN: 152098 Hom.: 515 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00473

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0540 AC: 8212 AN: 152214 Hom.: 514 Cov.: 32 AF XY: 0.0536 AC XY: 3991 AN XY: 74436

African (AFR) AF: 0.147 AC: 6098 AN: 41516

American (AMR) AF: 0.0449 AC: 687 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.146 AC: 754 AN: 5170

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4828

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00473 AC: 322 AN: 68008

Other (OTH) AF: 0.0489 AC: 103 AN: 2108

Alfa AF: 0.0240 Hom.: 90

Bravo AF: 0.0627

Asia WGS AF: 0.0870 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		0.97
Mutation Taster		=100/0	polymorphism (auto)

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: rs10114038; hg19: chr9-127327763;