14-33411008-A-G

Variant names:

• chr14-33411008-A-G
• rs12100538
• NM_001164749.2:c.468+43740A>G

Variant summary

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

The NM_001164749.2(NPAS3):​c.468+43740A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,948 control chromosomes in the GnomAD database, including 16,626 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 (16626 hom., cov: 32)
• Consequence: NPAS3 NM_001164749.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 1 publications found

Genes affected

NPAS3 (HGNC:19311): (neuronal PAS domain protein 3) This gene encodes a member of the basic helix-loop-helix and PAS domain-containing family of transcription factors. The encoded protein is localized to the nucleus and may regulate genes involved in neurogenesis. Chromosomal abnormalities that affect the coding potential of this gene are associated with schizophrenia and cognitive disability. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164749.2. 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
	NPAS3	NM_001164749.2	MANE Select	c.468+43740A>G		intron	N/A	NP_001158221.1	X5D2Q4
	NPAS3	NM_173159.3		c.429+43740A>G		intron	N/A	NP_775182.1	Q8IXF0-3
	NPAS3	NM_001394988.1		c.423+43740A>G		intron	N/A	NP_001381917.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPAS3	ENST00000356141.9	TSL:1 MANE Select	c.468+43740A>G		intron	N/A	ENSP00000348460.4	Q8IXF0-1
	NPAS3	ENST00000357798.9	TSL:1	c.429+43740A>G		intron	N/A	ENSP00000350446.5	Q8IXF0-3
	NPAS3	ENST00000548645.5	TSL:1	c.378+43740A>G		intron	N/A	ENSP00000448916.1	Q8IXF0-2

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68917 AN: 151830 Hom.: 16573 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.454 AC: 69034 AN: 151948 Hom.: 16626 Cov.: 32 AF XY: 0.458 AC XY: 33964 AN XY: 74238

African (AFR) AF: 0.614 AC: 25463 AN: 41446

American (AMR) AF: 0.502 AC: 7665 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2833 AN: 5132

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4814

European-Finnish (FIN) AF: 0.389 AC: 4100 AN: 10546

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23918 AN: 67954

Other (OTH) AF: 0.445 AC: 938 AN: 2108

Alfa AF: 0.392 Hom.: 6737

Bravo AF: 0.475

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.46
PhyloP100		-0.039
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: rs12100538; hg19: chr14-33880214;