rs10206927

Variant names:

• chr2-100851425-C-G
• rs10206927
• NM_002518.4:c.-23+31011C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-100851425-C-G
• chr2-100851425-C-T

Variant summary

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

The NM_002518.4(NPAS2):​c.-23+31011C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,268 control chromosomes in the GnomAD database, including 48,234 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 0.79 (48234 hom., cov: 33)
• Consequence: NPAS2 NM_002518.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002518.4. 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
	NPAS2	NM_002518.4	MANE Select	c.-23+31011C>G		intron	N/A	NP_002509.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPAS2	ENST00000335681.10	TSL:1 MANE Select	c.-23+31011C>G		intron	N/A	ENSP00000338283.5
	NPAS2	ENST00000427413.5	TSL:3	c.173+30226C>G		intron	N/A	ENSP00000397595.2

Frequencies

GnomAD3 genomes AF: 0.789 AC: 120092 AN: 152150 Hom.: 48190 Cov.: 33

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.789 AC: 120188 AN: 152268 Hom.: 48234 Cov.: 33 AF XY: 0.791 AC XY: 58924 AN XY: 74466

African (AFR) AF: 0.924 AC: 38431 AN: 41578

American (AMR) AF: 0.622 AC: 9506 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4084 AN: 5172

South Asian (SAS) AF: 0.803 AC: 3878 AN: 4830

European-Finnish (FIN) AF: 0.836 AC: 8881 AN: 10622

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50429 AN: 67998

Other (OTH) AF: 0.781 AC: 1650 AN: 2112

Alfa AF: 0.767 Hom.: 5658

Bravo AF: 0.776

Asia WGS AF: 0.782 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.12
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: rs10206927; hg19: chr2-101467887;