chr1-6109946-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_015557.3(CHD5):c.5427C>T(p.Ala1809=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,589,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
CHD5
NM_015557.3 synonymous
NM_015557.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.84
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 1-6109946-G-A is Benign according to our data. Variant chr1-6109946-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 750465.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-4.84 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000217 (33/152270) while in subpopulation AFR AF= 0.000506 (21/41542). AF 95% confidence interval is 0.000338. There are 0 homozygotes in gnomad4. There are 14 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 33 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD5 | NM_015557.3 | c.5427C>T | p.Ala1809= | synonymous_variant | 38/42 | ENST00000262450.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD5 | ENST00000262450.8 | c.5427C>T | p.Ala1809= | synonymous_variant | 38/42 | 1 | NM_015557.3 | P1 | |
CHD5 | ENST00000462991.5 | c.*499C>T | 3_prime_UTR_variant, NMD_transcript_variant | 28/31 | 1 | ||||
CHD5 | ENST00000377999.5 | c.*1997C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/21 | 2 | ||||
CHD5 | ENST00000496404.1 | c.*467C>T | 3_prime_UTR_variant, NMD_transcript_variant | 30/34 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152152Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000763 AC: 17AN: 222852Hom.: 0 AF XY: 0.0000500 AC XY: 6AN XY: 119890
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GnomAD4 exome AF: 0.000111 AC: 159AN: 1437220Hom.: 0 Cov.: 32 AF XY: 0.0000869 AC XY: 62AN XY: 713136
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at