rs39075

Variant names:

• chr7-29237076-G-A
• rs39075
• NM_004067.4:c.49+42086G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-29237076-G-A
• chr7-29237076-G-C
• chr7-29237076-G-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+42086G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,026 control chromosomes in the GnomAD database, including 13,075 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 0.41 (13075 hom., cov: 33)
• Consequence: CHN2 NM_004067.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 17 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 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+42086G>A		intron	N/A	NP_004058.1	P52757-1
	CHN2	NM_001293070.2		c.49+42086G>A		intron	N/A	NP_001279999.1	B7Z1V0
	CHN2	NM_001293072.2		c.4+39093G>A		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+42086G>A		intron	N/A	ENSP00000222792.7	P52757-1
	CHN2	ENST00000706161.1		c.49+42086G>A		intron	N/A	ENSP00000516239.1	A0A994J7L4
	CHN2	ENST00000409350.6	TSL:4	c.49+42086G>A		intron	N/A	ENSP00000386968.2	B7Z1V0

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62666 AN: 151908 Hom.: 13059 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.413 AC: 62725 AN: 152026 Hom.: 13075 Cov.: 33 AF XY: 0.410 AC XY: 30492 AN XY: 74296

African (AFR) AF: 0.425 AC: 17635 AN: 41460

American (AMR) AF: 0.445 AC: 6804 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3472

East Asian (EAS) AF: 0.390 AC: 2014 AN: 5160

South Asian (SAS) AF: 0.388 AC: 1871 AN: 4820

European-Finnish (FIN) AF: 0.392 AC: 4132 AN: 10552

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27164 AN: 67962

Other (OTH) AF: 0.404 AC: 852 AN: 2108

Alfa AF: 0.404 Hom.: 7143

Bravo AF: 0.416

Asia WGS AF: 0.382 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.8
DANN	Benign	0.54
PhyloP100		-0.75
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: rs39075; hg19: chr7-29276692;