chr1-6132116-ATGCCCACCCCCTTAC-A

Variant names:

• chr1-6132116-ATGCCCACCCCCTTAC-A
• NM_015557.3:c.3145-383_3145-369delGTAAGGGGGTGGGCA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015557.3(CHD5):​c.3145-383_3145-369delGTAAGGGGGTGGGCA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHD5 NM_015557.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHD5	NM_015557.3	c.3145-383_3145-369delGTAAGGGGGTGGGCA		intron_variant	Intron 20 of 41	ENST00000262450.8	NP_056372.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD5	ENST00000262450.8	c.3145-383_3145-369delGTAAGGGGGTGGGCA		intron_variant	Intron 20 of 41	1	NM_015557.3	ENSP00000262450.3
CHD5	ENST00000462991.5	n.1291-383_1291-369delGTAAGGGGGTGGGCA		intron_variant	Intron 9 of 30	1		ENSP00000466706.1
CHD5	ENST00000496404.1	n.3145-383_3145-369delGTAAGGGGGTGGGCA		intron_variant	Intron 20 of 33	2		ENSP00000433676.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-6192176;