2-100921242-G-A

Position:

• chr2-100921242-G-A

Variant summary

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

The NM_002518.4(NPAS2):​c.33-3904G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,156 control chromosomes in the GnomAD database, including 5,029 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 0.24 (5029 hom., cov: 32)
• Consequence: NPAS2 NM_002518.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPAS2	NM_002518.4	c.33-3904G>A		intron_variant		ENST00000335681.10	NP_002509.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPAS2	ENST00000335681.10	c.33-3904G>A		intron_variant		1	NM_002518.4	ENSP00000338283	P1
NPAS2	ENST00000427413.5	c.228-3904G>A		intron_variant		3		ENSP00000397595

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35877 AN: 152038 Hom.: 5025 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.236 AC: 35899 AN: 152156 Hom.: 5029 Cov.: 32 AF XY: 0.234 AC XY: 17380 AN XY: 74368

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.236

Alfa AF: 0.204 Hom.: 606

Bravo AF: 0.246

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.42

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: rs6725296; hg19: chr2-101537704;