rs39118

Variant names:

• chr7-29314416-C-A
• rs39118
• NM_004067.4:c.50-40209C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-29314416-C-A
• chr7-29314416-C-G

Variant summary

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

The NM_004067.4(CHN2):​c.50-40209C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,242 control chromosomes in the GnomAD database, including 61,361 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 0.90 (61361 hom., cov: 32)
• Consequence: CHN2 NM_004067.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 9 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004067.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHN2	NM_004067.4	MANE Select	c.50-40209C>A		intron	N/A	NP_004058.1
	CHN2	NM_001293070.2		c.88+21453C>A		intron	N/A	NP_001279999.1
	CHN2	NM_001293072.2		c.5-40209C>A		intron	N/A	NP_001280001.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHN2	ENST00000222792.11	TSL:1 MANE Select	c.50-40209C>A		intron	N/A	ENSP00000222792.7
	CHN2	ENST00000706161.1		c.127+20808C>A		intron	N/A	ENSP00000516239.1
	CHN2	ENST00000409350.6	TSL:4	c.88+21453C>A		intron	N/A	ENSP00000386968.2

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136441 AN: 152124 Hom.: 61307 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.897 AC: 136553 AN: 152242 Hom.: 61361 Cov.: 32 AF XY: 0.897 AC XY: 66759 AN XY: 74424

African (AFR) AF: 0.920 AC: 38206 AN: 41550

American (AMR) AF: 0.915 AC: 13992 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2931 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5157 AN: 5176

South Asian (SAS) AF: 0.790 AC: 3809 AN: 4820

European-Finnish (FIN) AF: 0.900 AC: 9541 AN: 10604

Middle Eastern (MID) AF: 0.832 AC: 243 AN: 292

European-Non Finnish (NFE) AF: 0.882 AC: 59964 AN: 68012

Other (OTH) AF: 0.901 AC: 1902 AN: 2112

Alfa AF: 0.878 Hom.: 33200

Bravo AF: 0.904

Asia WGS AF: 0.903 AC: 3140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.010
DANN	Benign	0.62
PhyloP100		-1.8
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: rs39118; hg19: chr7-29354032;