Variant rs17029184 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_015557.3(CHD5):c.3336G>A(p.Ala1112=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 1,613,710 control chromosomes in the GnomAD database, including 8,038 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 0.069 ( 639 hom., cov: 32)

Exomes 𝑓: 0.085 ( 7399 hom. )

Consequence

CHD5
NM_015557.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.67

Variant links:

Genes affected

CHD5 (HGNC:16816): (chromodomain helicase DNA binding protein 5) This gene encodes a member of the chromodomain helicase DNA-binding protein family. Members of this family are characterized by a chromodomain, a helicase ATP-binding domain and an additional functional domain. This gene encodes a neuron-specific protein that may function in chromatin remodeling and gene transcription. This gene is a potential tumor suppressor gene that may play a role in the development of neuroblastoma. [provided by RefSeq, Feb 2012]

CHD5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP7

Synonymous conserved (PhyloP=-4.67 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHD5	NM_015557.3 linkuse as main transcript	c.3336G>A	p.Ala1112=	synonymous_variant	22/42	ENST00000262450.8	NP_056372.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CHD5	ENST00000262450.8 linkuse as main transcript	c.3336G>A	p.Ala1112=	synonymous_variant	22/42	1	NM_015557.3	ENSP00000262450	P1
CHD5	ENST00000462991.5 linkuse as main transcript	c.1485G>A	p.Ala495=	synonymous_variant, NMD_transcript_variant	11/31	1		ENSP00000466706
CHD5	ENST00000496404.1 linkuse as main transcript	c.3336G>A	p.Ala1112=	synonymous_variant, NMD_transcript_variant	22/34	2		ENSP00000433676
CHD5	ENST00000377999.5 linkuse as main transcript	c.183G>A	p.Ala61=	synonymous_variant, NMD_transcript_variant	2/21	2		ENSP00000367238

Frequencies

GnomAD3 genomes

AF:

0.0695

AC:

10567

AN:

152004

Hom.:

643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0159

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0485

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.0749

Gnomad FIN

AF:

0.0926

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0839

Gnomad OTH

AF:

0.0560

GnomAD3 exomes

AF:

0.0866

AC:

21742

AN:

251162

Hom.:

1626

AF XY:

0.0867

AC XY:

11774

AN XY:

135796

show subpopulations

Gnomad AFR exome

AF:

0.0157

Gnomad AMR exome

AF:

0.0365

Gnomad ASJ exome

AF:

0.0389

Gnomad EAS exome

AF:

0.337

Gnomad SAS exome

AF:

0.0691

Gnomad FIN exome

AF:

0.0901

Gnomad NFE exome

AF:

0.0805

Gnomad OTH exome

AF:

0.0717

GnomAD4 exome

AF:

0.0855

AC:

124958

AN:

1461588

Hom.:

7399

Cov.:

AF XY:

0.0851

AC XY:

61867

AN XY:

727110

show subpopulations

Gnomad4 AFR exome

AF:

0.0120

Gnomad4 AMR exome

AF:

0.0370

Gnomad4 ASJ exome

AF:

0.0375

Gnomad4 EAS exome

AF:

0.369

Gnomad4 SAS exome

AF:

0.0700

Gnomad4 FIN exome

AF:

0.0909

Gnomad4 NFE exome

AF:

0.0822

Gnomad4 OTH exome

AF:

0.0807

GnomAD4 genome

AF:

0.0694

AC:

10559

AN:

152122

Hom.:

639

Cov.:

AF XY:

0.0713

AC XY:

5301

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.0159

Gnomad4 AMR

AF:

0.0484

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.346

Gnomad4 SAS

AF:

0.0752

Gnomad4 FIN

AF:

0.0926

Gnomad4 NFE

AF:

0.0838

Gnomad4 OTH

AF:

0.0555

Alfa

AF:

0.0710

Hom.:

267

Bravo

AF:

0.0639

Asia WGS

AF:

0.180

AC:

624

AN:

3478

EpiCase

AF:

0.0735

EpiControl

AF:

0.0732

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.7

DANN

Benign

0.74

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over