NM_014947.5:c.45-4990G>T

Variant names:

• chr1-42283662-C-A
• rs1125792
• NM_014947.5:c.45-4990G>T

Variant summary

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

The NM_014947.5(FOXJ3):​c.45-4990G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,042 control chromosomes in the GnomAD database, including 40,981 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 0.73 (40981 hom., cov: 31)
• Consequence: FOXJ3 NM_014947.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

FOXJ3 (HGNC:29178): (forkhead box J3) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXJ3	NM_014947.5	c.45-4990G>T		intron_variant	Intron 2 of 12	ENST00000361346.6	NP_055762.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXJ3	ENST00000361346.6	c.45-4990G>T		intron_variant	Intron 2 of 12	1	NM_014947.5	ENSP00000354620.1

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111260 AN: 151924 Hom.: 40940 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.732 AC: 111361 AN: 152042 Hom.: 40981 Cov.: 31 AF XY: 0.734 AC XY: 54576 AN XY: 74324

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.754

Alfa AF: 0.739 Hom.: 5173

Bravo AF: 0.735

Asia WGS AF: 0.657 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.46

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: rs1125792; hg19: chr1-42749333; COSMIC: COSV62361051;