rs1016726

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004067.4(CHN2):​c.50-37838G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,044 control chromosomes in the GnomAD database, including 1,329 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 0.12 ( 1329 hom., cov: 32)

Consequence

CHN2
NM_004067.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.319
Variant links:
Genes affected
CHN2 (HGNC:1944): (chimerin 2) This gene encodes a guanosine triphosphate (GTP)-metabolizing protein that contains a phorbol-ester/diacylglycerol (DAG)-type zinc finger, a Rho-GAP domain, and an SH2 domain. The encoded protein translocates from the cytosol to the Golgi apparatus membrane upon binding by diacylglycerol (DAG). Activity of this protein is important in cell proliferation and migration, and expression changes in this gene have been detected in cancers. A mutation in this gene has also been associated with schizophrenia in men. Alternative transcript splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, May 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHN2NM_004067.4 linkuse as main transcriptc.50-37838G>A intron_variant ENST00000222792.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHN2ENST00000222792.11 linkuse as main transcriptc.50-37838G>A intron_variant 1 NM_004067.4 P1P52757-1

Frequencies

GnomAD3 genomes
AF:
0.125
AC:
18941
AN:
151926
Hom.:
1328
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.187
Gnomad AMI
AF:
0.0817
Gnomad AMR
AF:
0.157
Gnomad ASJ
AF:
0.0842
Gnomad EAS
AF:
0.203
Gnomad SAS
AF:
0.0825
Gnomad FIN
AF:
0.0659
Gnomad MID
AF:
0.184
Gnomad NFE
AF:
0.0879
Gnomad OTH
AF:
0.138
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.125
AC:
18961
AN:
152044
Hom.:
1329
Cov.:
32
AF XY:
0.124
AC XY:
9207
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.187
Gnomad4 AMR
AF:
0.157
Gnomad4 ASJ
AF:
0.0842
Gnomad4 EAS
AF:
0.203
Gnomad4 SAS
AF:
0.0826
Gnomad4 FIN
AF:
0.0659
Gnomad4 NFE
AF:
0.0879
Gnomad4 OTH
AF:
0.138
Alfa
AF:
0.0984
Hom.:
1676
Bravo
AF:
0.136
Asia WGS
AF:
0.153
AC:
532
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
4.8
DANN
Benign
0.51

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

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

Other links and lift over

dbSNP: rs1016726; hg19: chr7-29356403; API