rs356642

Positions:

• chr2-100920976-A-G

Variant summary

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

The NM_002518.4(NPAS2):​c.33-4170A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,286 control chromosomes in the GnomAD database, including 56,690 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 0.86 (56690 hom., cov: 34)
• Consequence: NPAS2 NM_002518.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

NPAS2 (HGNC:7895): (neuronal PAS domain protein 2) The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH)-PAS family of transcription factors. A similar mouse protein may play a regulatory role in the acquisition of specific types of memory. It also may function as a part of a molecular clock operative in the mammalian forebrain. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPAS2	NM_002518.4	c.33-4170A>G		intron_variant		ENST00000335681.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPAS2	ENST00000335681.10	c.33-4170A>G		intron_variant		1	NM_002518.4	P1
NPAS2	ENST00000427413.5	c.228-4170A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131141 AN: 152168 Hom.: 56638 Cov.: 34

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.862 AC: 131254 AN: 152286 Hom.: 56690 Cov.: 34 AF XY: 0.868 AC XY: 64604 AN XY: 74464

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.857

Alfa AF: 0.834 Hom.: 102562

Bravo AF: 0.861

Asia WGS AF: 0.943 AC: 3279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.20

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: rs356642; hg19: chr2-101537438;