rs2455084

Variant names:

• chr1-42315846-T-A
• rs2455084
• NM_014947.5:c.-17-4736A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-42315846-T-A
• chr1-42315846-T-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.-17-4736A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,148 control chromosomes in the GnomAD database, including 41,342 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 0.74 (41342 hom., cov: 33)
• Consequence: FOXJ3 NM_014947.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 2 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]

ENSG00000294990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.796 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXJ3	NM_014947.5	MANE Select	c.-17-4736A>T		intron	N/A	NP_055762.3
	FOXJ3	NM_001198850.2		c.-17-4736A>T		intron	N/A	NP_001185779.1
	FOXJ3	NM_001198851.2		c.-127-391A>T		intron	N/A	NP_001185780.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXJ3	ENST00000361346.6	TSL:1 MANE Select	c.-17-4736A>T		intron	N/A	ENSP00000354620.1
	FOXJ3	ENST00000372572.5	TSL:1	c.-127-391A>T		intron	N/A	ENSP00000361653.1
	FOXJ3	ENST00000445886.5	TSL:1	c.-17-4736A>T		intron	N/A	ENSP00000393408.1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111832 AN: 152030 Hom.: 41303 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.736 AC: 111933 AN: 152148 Hom.: 41342 Cov.: 33 AF XY: 0.737 AC XY: 54856 AN XY: 74398

African (AFR) AF: 0.668 AC: 27694 AN: 41488

American (AMR) AF: 0.808 AC: 12360 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3835 AN: 5164

South Asian (SAS) AF: 0.665 AC: 3207 AN: 4824

European-Finnish (FIN) AF: 0.795 AC: 8423 AN: 10596

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51127 AN: 67990

Other (OTH) AF: 0.758 AC: 1597 AN: 2108

Alfa AF: 0.742 Hom.: 5207

Bravo AF: 0.739

Asia WGS AF: 0.652 AC: 2271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.56
PhyloP100		0.14
PromoterAI		0.010	Neutral
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: rs2455084; hg19: chr1-42781517;