GeneBe

NM_001144990.2:c.241-8648T>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001144990.2(NWD2):​c.241-8648T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,148 control chromosomes in the GnomAD database, including 5,761 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 0.26 ( 5761 hom., cov: 33)

Consequence

NWD2
NM_001144990.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.386

Publications

6 publications found
Variant links:
Genes affected
NWD2 (HGNC:29229): (NACHT and WD repeat domain containing 2)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NWD2NM_001144990.2 linkc.241-8648T>C intron_variant Intron 2 of 6 ENST00000309447.6 NP_001138462.1 Q9ULI1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NWD2ENST00000309447.6 linkc.241-8648T>C intron_variant Intron 2 of 6 5 NM_001144990.2 ENSP00000309501.5 Q9ULI1

Frequencies

GnomAD3 genomes
AF:
0.259
AC:
39389
AN:
152030
Hom.:
5752
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.154
Gnomad AMI
AF:
0.322
Gnomad AMR
AF:
0.408
Gnomad ASJ
AF:
0.236
Gnomad EAS
AF:
0.403
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.268
Gnomad MID
AF:
0.258
Gnomad NFE
AF:
0.275
Gnomad OTH
AF:
0.294
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.259
AC:
39417
AN:
152148
Hom.:
5761
Cov.:
33
AF XY:
0.263
AC XY:
19581
AN XY:
74380
show subpopulations
African (AFR)
AF:
0.154
AC:
6408
AN:
41542
American (AMR)
AF:
0.408
AC:
6234
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.236
AC:
819
AN:
3472
East Asian (EAS)
AF:
0.403
AC:
2085
AN:
5168
South Asian (SAS)
AF:
0.284
AC:
1369
AN:
4824
European-Finnish (FIN)
AF:
0.268
AC:
2840
AN:
10584
Middle Eastern (MID)
AF:
0.243
AC:
71
AN:
292
European-Non Finnish (NFE)
AF:
0.275
AC:
18673
AN:
67968
Other (OTH)
AF:
0.295
AC:
624
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1485
2970
4456
5941
7426
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
396
792
1188
1584
1980
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.245
Hom.:
2866
Bravo
AF:
0.268
Asia WGS
AF:
0.325
AC:
1130
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
7.9
DANN
Benign
0.88
PhyloP100
0.39
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

Publications

Other links and lift over

dbSNP: rs12505080; hg19: chr4-37349340; API