rs121912792

Variant names:

• chr2-174944942-T-A
• rs121912792
• NM_001822.7:c.60A>T

Your query was ambiguous. Multiple possible variants found:

• chr2-174944942-T-A
• chr2-174944942-T-C

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PP2 PP5

The NM_001822.7(CHN1):​c.60A>T​(p.Leu20Phe) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHN1 NM_001822.7 missense, splice_region
• Scores: Splicing: ADA: 0.00003479
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: -0.341
• Publications: 5 publications found

Genes affected

CHN1 (HGNC:1943): (chimerin 1) This gene encodes GTPase-activating protein for ras-related p21-rac and a phorbol ester receptor. It is predominantly expressed in neurons, and plays an important role in neuronal signal-transduction mechanisms. Mutations in this gene are associated with Duane's retraction syndrome 2 (DURS2). Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Apr 2011]

CHN1 Gene-Disease associations (from GenCC):

• Duane retraction syndrome 2

  Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen
• Duane retraction syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 13 curated pathogenic missense variants (we use a threshold of 10). The gene has 2 curated benign missense variants. Gene score misZ: 1.2662 (below the threshold of 3.09). Trascript score misZ: 1.5101 (below the threshold of 3.09). GenCC associations: The gene is linked to Duane retraction syndrome 2, Duane retraction syndrome.
• PP5: Variant 2-174944942-T-A is Pathogenic according to our data. Variant chr2-174944942-T-A is described in ClinVar as Pathogenic. ClinVar VariationId is 17550.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001822.7. 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
	CHN1	NM_001822.7	MANE Select	c.60A>T	p.Leu20Phe	missense splice_region	Exon 3 of 13	NP_001813.1	P15882-1
	CHN1	NM_001371513.1		c.60A>T	p.Leu20Phe	missense splice_region	Exon 4 of 14	NP_001358442.1	P15882-1
	CHN1	NM_001025201.4		c.60A>T	p.Leu20Phe	missense splice_region	Exon 4 of 13	NP_001020372.2	P15882-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHN1	ENST00000409900.9	TSL:1 MANE Select	c.60A>T	p.Leu20Phe	missense splice_region	Exon 3 of 13	ENSP00000386741.4	P15882-1
	CHN1	ENST00000934192.1		c.60A>T	p.Leu20Phe	missense splice_region	Exon 3 of 14	ENSP00000604251.1
	CHN1	ENST00000409156.7	TSL:2	c.60A>T	p.Leu20Phe	missense splice_region	Exon 4 of 13	ENSP00000386470.3	P15882-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Duane retraction syndrome 2 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Benign	18
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.52	D
Eigen	Benign	-0.16
Eigen_PC	Benign	-0.32
FATHMM_MKL	Benign	0.49	N
LIST_S2	Uncertain	0.95	D
M_CAP	Uncertain	0.13	D
MetaRNN	Uncertain	0.55	D
MetaSVM	Uncertain	-0.073	T
MutationAssessor	Uncertain	2.7	M
PhyloP100		-0.34
PrimateAI	Pathogenic	0.80	D
PROVEAN	Uncertain	-2.5	N
REVEL	Uncertain	0.49
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0030	D
Polyphen		0.97	D
Vest4		0.65
MutPred		0.58		Loss of helix (P = 0.1299)
MVP		0.84
MPC		0.60
ClinPred		0.91	D
GERP RS		-6.5
Varity_R		0.52
gMVP		0.53
Mutation Taster		=34/66	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000035
dbscSNV1_RF	Benign	0.17
Splicevardb		2.0
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: rs121912792; hg19: chr2-175809670;