chr1-42191148-T-A

Variant names:

• chr1-42191148-T-A
• rs16829212
• NM_014947.5:c.1351+155A>T

Variant summary

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

The NM_014947.5(FOXJ3):​c.1351+155A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,790 control chromosomes in the GnomAD database, including 17,372 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 0.45 (17372 hom., cov: 33)
• Consequence: FOXJ3 NM_014947.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 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.1351+155A>T		intron	N/A	NP_055762.3
	FOXJ3	NM_001198850.2		c.1351+155A>T		intron	N/A	NP_001185779.1
	FOXJ3	NM_001198851.2		c.1351+155A>T		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.1351+155A>T		intron	N/A	ENSP00000354620.1
	FOXJ3	ENST00000372572.5	TSL:1	c.1351+155A>T		intron	N/A	ENSP00000361653.1
	FOXJ3	ENST00000372573.5	TSL:2	c.1351+155A>T		intron	N/A	ENSP00000361654.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67746 AN: 151670 Hom.: 17371 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.446 AC: 67760 AN: 151790 Hom.: 17372 Cov.: 33 AF XY: 0.446 AC XY: 33100 AN XY: 74188

African (AFR) AF: 0.181 AC: 7487 AN: 41330

American (AMR) AF: 0.498 AC: 7600 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2282 AN: 3468

East Asian (EAS) AF: 0.511 AC: 2635 AN: 5154

South Asian (SAS) AF: 0.407 AC: 1951 AN: 4790

European-Finnish (FIN) AF: 0.589 AC: 6212 AN: 10554

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37976 AN: 67936

Other (OTH) AF: 0.489 AC: 1029 AN: 2104

Alfa AF: 0.498 Hom.: 2563

Bravo AF: 0.434

Asia WGS AF: 0.400 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.4
DANN	Benign	0.76
PhyloP100		0.26
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: rs16829212; hg19: chr1-42656819;