rs58728948

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002518.4(NPAS2):​c.2068G>A​(p.Ala690Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,614,170 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0091 ( 22 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 18 hom. )

Consequence

NPAS2
NM_002518.4 missense

Scores

2
16

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.68
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0067507327).
BP6
Variant 2-100990829-G-A is Benign according to our data. Variant chr2-100990829-G-A is described in ClinVar as [Benign]. Clinvar id is 791865.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00905 (1379/152316) while in subpopulation AFR AF= 0.031 (1288/41572). AF 95% confidence interval is 0.0296. There are 22 homozygotes in gnomad4. There are 664 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1379 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NPAS2NM_002518.4 linkuse as main transcriptc.2068G>A p.Ala690Thr missense_variant 19/21 ENST00000335681.10 NP_002509.2 Q99743A2I2P5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NPAS2ENST00000335681.10 linkuse as main transcriptc.2068G>A p.Ala690Thr missense_variant 19/211 NM_002518.4 ENSP00000338283.5 Q99743

Frequencies

GnomAD3 genomes
AF:
0.00907
AC:
1380
AN:
152198
Hom.:
23
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0311
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00321
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000353
Gnomad OTH
AF:
0.00717
GnomAD3 exomes
AF:
0.00254
AC:
637
AN:
251234
Hom.:
6
AF XY:
0.00203
AC XY:
276
AN XY:
135834
show subpopulations
Gnomad AFR exome
AF:
0.0314
Gnomad AMR exome
AF:
0.00191
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.000229
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000370
Gnomad OTH exome
AF:
0.00179
GnomAD4 exome
AF:
0.00104
AC:
1519
AN:
1461854
Hom.:
18
Cov.:
31
AF XY:
0.000891
AC XY:
648
AN XY:
727230
show subpopulations
Gnomad4 AFR exome
AF:
0.0303
Gnomad4 AMR exome
AF:
0.00230
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000139
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000201
Gnomad4 OTH exome
AF:
0.00240
GnomAD4 genome
AF:
0.00905
AC:
1379
AN:
152316
Hom.:
22
Cov.:
33
AF XY:
0.00892
AC XY:
664
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.0310
Gnomad4 AMR
AF:
0.00320
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000353
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00188
Hom.:
7
Bravo
AF:
0.0108
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.0306
AC:
135
ESP6500EA
AF:
0.000814
AC:
7
ExAC
AF:
0.00323
AC:
392
Asia WGS
AF:
0.00318
AC:
11
AN:
3478
EpiCase
AF:
0.000654
EpiControl
AF:
0.000533

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.50
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.057
T
Eigen
Benign
-0.23
Eigen_PC
Benign
-0.29
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.68
T
MetaRNN
Benign
0.0068
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.7
L
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-0.55
N
REVEL
Benign
0.077
Sift
Benign
0.045
D
Sift4G
Benign
0.18
T
Polyphen
0.29
B
Vest4
0.36
MVP
0.26
MPC
0.28
ClinPred
0.0037
T
GERP RS
3.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.043
gMVP
0.27

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs58728948; hg19: chr2-101607291; API