rs1555437429

Positions:

• chr15-92924493-C-A
• chr15-92924493-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 5P and 2B. PM2 PM5 PP2 BP4_Moderate

The NM_001271.4(CHD2):​c.235C>A​(p.Leu79Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L79P) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHD2 NM_001271.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

CHD2 (HGNC:1917): (chromodomain helicase DNA binding protein 2) The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr15-92924494-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 2999776.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1}.
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CHD2. . Gene score misZ 5.2052 (greater than the threshold 3.09). Trascript score misZ 6.0204 (greater than threshold 3.09). GenCC has associacion of gene with developmental and epileptic encephalopathy 94, complex neurodevelopmental disorder, myoclonic-astatic epilepsy, Lennox-Gastaut syndrome.
• BP4: Computational evidence support a benign effect (MetaRNN=0.14357176).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHD2	NM_001271.4	c.235C>A	p.Leu79Ile	missense_variant	3/39	ENST00000394196.9
CHD2	NM_001042572.3	c.235C>A	p.Leu79Ile	missense_variant	3/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHD2	ENST00000394196.9	c.235C>A	p.Leu79Ile	missense_variant	3/39	5	NM_001271.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.063
BayesDel_addAF	Benign	-0.035	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	22
DANN	Benign	0.96
DEOGEN2	Benign	0.062	.;.;T;T;.;T
Eigen	Benign	-0.21
Eigen_PC	Benign	-0.0076
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.85	D;D;D;D;D;D
M_CAP	Benign	0.065	D
MetaRNN	Benign	0.14	T;T;T;T;T;T
MetaSVM	Benign	-0.50	T
MutationAssessor	Benign	0.69	.;N;N;.;N;.
MutationTaster	Benign	0.98	N;N;N;N
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-0.12	.;.;N;.;N;.
REVEL	Benign	0.12
Sift	Benign	0.38	.;.;T;.;T;.
Sift4G	Benign	0.18	T;T;T;T;T;T
Polyphen		0.13, 0.023, 0.089	.;B;B;.;.;B
Vest4		0.17, 0.16, 0.25, 0.19
MutPred		0.19		Gain of MoRF binding (P = 0.0955);Gain of MoRF binding (P = 0.0955);Gain of MoRF binding (P = 0.0955);Gain of MoRF binding (P = 0.0955);Gain of MoRF binding (P = 0.0955);.;
MVP		0.44
MPC		0.81
ClinPred		0.27	T
GERP RS		4.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.13
gMVP		0.089

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

Other links and lift over

dbSNP: rs1555437429; hg19: chr15-93467723;