7-29205143-C-T

Variant names:

• chr7-29205143-C-T
• rs3812389
• NM_004067.4:c.49+10153C>T

Variant summary

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

The NM_004067.4(CHN2):​c.49+10153C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,212 control chromosomes in the GnomAD database, including 2,693 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 0.18 (2693 hom., cov: 32)
• Consequence: CHN2 NM_004067.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 8 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]

CHN2-AS1 (HGNC:40149): (CHN2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.217 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.49+10153C>T		intron	N/A	NP_004058.1	P52757-1
	CHN2	NM_001293070.2		c.49+10153C>T		intron	N/A	NP_001279999.1	B7Z1V0
	CHN2	NM_001293072.2		c.4+7160C>T		intron	N/A	NP_001280001.1	B7Z1W9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHN2	ENST00000222792.11	TSL:1 MANE Select	c.49+10153C>T		intron	N/A	ENSP00000222792.7	P52757-1
	CHN2	ENST00000706161.1		c.49+10153C>T		intron	N/A	ENSP00000516239.1	A0A994J7L4
	CHN2	ENST00000409350.6	TSL:4	c.49+10153C>T		intron	N/A	ENSP00000386968.2	B7Z1V0

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27109 AN: 152094 Hom.: 2689 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.178 AC: 27115 AN: 152212 Hom.: 2693 Cov.: 32 AF XY: 0.175 AC XY: 13001 AN XY: 74426

African (AFR) AF: 0.0872 AC: 3624 AN: 41548

American (AMR) AF: 0.223 AC: 3407 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3470

East Asian (EAS) AF: 0.186 AC: 964 AN: 5174

South Asian (SAS) AF: 0.188 AC: 909 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1630 AN: 10588

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14932 AN: 67994

Other (OTH) AF: 0.203 AC: 429 AN: 2116

Alfa AF: 0.209 Hom.: 14876

Bravo AF: 0.180

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.45
PhyloP100		0.071
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: rs3812389; hg19: chr7-29244759;