chr1-42244433-T-C

Variant names:

• chr1-42244433-T-C
• rs12732892
• NM_014947.5:c.445-16467A>G

Variant summary

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

The NM_014947.5(FOXJ3):​c.445-16467A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,162 control chromosomes in the GnomAD database, including 2,008 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 0.14 (2008 hom., cov: 32)
• Consequence: FOXJ3 NM_014947.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014947.5. 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
	FOXJ3	NM_014947.5	MANE Select	c.445-16467A>G		intron	N/A	NP_055762.3
	FOXJ3	NM_001198850.2		c.445-16467A>G		intron	N/A	NP_001185779.1
	FOXJ3	NM_001198851.2		c.445-16467A>G		intron	N/A	NP_001185780.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXJ3	ENST00000361346.6	TSL:1 MANE Select	c.445-16467A>G		intron	N/A	ENSP00000354620.1
	FOXJ3	ENST00000372572.5	TSL:1	c.445-16467A>G		intron	N/A	ENSP00000361653.1
	FOXJ3	ENST00000445886.5	TSL:1	c.445-16467A>G		intron	N/A	ENSP00000393408.1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21835 AN: 152044 Hom.: 2009 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.143 AC: 21834 AN: 152162 Hom.: 2008 Cov.: 32 AF XY: 0.146 AC XY: 10839 AN XY: 74370

African (AFR) AF: 0.0365 AC: 1515 AN: 41552

American (AMR) AF: 0.118 AC: 1806 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3470

East Asian (EAS) AF: 0.175 AC: 904 AN: 5170

South Asian (SAS) AF: 0.244 AC: 1175 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1863 AN: 10582

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13585 AN: 67964

Other (OTH) AF: 0.133 AC: 281 AN: 2108

Alfa AF: 0.159 Hom.: 360

Bravo AF: 0.130

Asia WGS AF: 0.242 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.78
PhyloP100		0.19
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: rs12732892; hg19: chr1-42710104;