rs7179432

Variant names:

• chr15-93021742-T-C
• rs7179432
• ENST00000626874.2:c.*1417T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-93021742-T-C
• chr15-93021742-T-G

Variant summary

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

The ENST00000626874.2(CHD2):​c.*1417T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,016 control chromosomes in the GnomAD database, including 16,681 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 0.45 (16680 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: CHD2 ENST00000626874.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 6 publications found

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]

CHD2 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• developmental and epileptic encephalopathy 94

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• Lennox-Gastaut syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• myoclonic-astatic epilepsy

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626874.2. 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
	CHD2	NM_001271.4	MANE Select	c.5153+1484T>C		intron	N/A	NP_001262.3	O14647-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHD2	ENST00000626874.2	TSL:1	c.*1417T>C		3_prime_UTR	Exon 38 of 38	ENSP00000486629.1	O14647-2
	CHD2	ENST00000394196.9	TSL:5 MANE Select	c.5153+1484T>C		intron	N/A	ENSP00000377747.4	O14647-1
	CHD2	ENST00000625662.3	TSL:5	n.*1324+1484T>C		intron	N/A	ENSP00000486007.2	A0A0D9SEU0

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68558 AN: 151896 Hom.: 16666 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.441

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.451 AC: 68594 AN: 152014 Hom.: 16680 Cov.: 32 AF XY: 0.462 AC XY: 34345 AN XY: 74292

African (AFR) AF: 0.321 AC: 13320 AN: 41448

American (AMR) AF: 0.512 AC: 7823 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1320 AN: 3464

East Asian (EAS) AF: 0.896 AC: 4647 AN: 5188

South Asian (SAS) AF: 0.585 AC: 2816 AN: 4814

European-Finnish (FIN) AF: 0.602 AC: 6338 AN: 10536

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30927 AN: 67966

Other (OTH) AF: 0.448 AC: 947 AN: 2114

Alfa AF: 0.443 Hom.: 33013

Bravo AF: 0.437

Asia WGS AF: 0.700 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.72
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7179432; hg19: chr15-93564972;