NM_017780.4:c.6103+8C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017780.4(CHD7):c.6103+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0572 in 1,613,390 control chromosomes in the GnomAD database, including 7,029 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_017780.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHD7 | ENST00000423902.7 | c.6103+8C>T | splice_region_variant, intron_variant | Intron 30 of 37 | 5 | NM_017780.4 | ENSP00000392028.1 | |||
CHD7 | ENST00000524602.5 | c.1717-9515C>T | intron_variant | Intron 2 of 4 | 1 | ENSP00000437061.1 | ||||
CHD7 | ENST00000695853.1 | n.6103+8C>T | splice_region_variant, intron_variant | Intron 30 of 36 | ENSP00000512218.1 |
Frequencies
GnomAD3 genomes AF: 0.138 AC: 20950AN: 151966Hom.: 3120 Cov.: 32
GnomAD3 exomes AF: 0.0662 AC: 16489AN: 249032Hom.: 1462 AF XY: 0.0611 AC XY: 8257AN XY: 135124
GnomAD4 exome AF: 0.0488 AC: 71363AN: 1461306Hom.: 3908 Cov.: 32 AF XY: 0.0476 AC XY: 34633AN XY: 726954
GnomAD4 genome AF: 0.138 AC: 20973AN: 152084Hom.: 3121 Cov.: 32 AF XY: 0.137 AC XY: 10165AN XY: 74350
ClinVar
Submissions by phenotype
not specified Benign:9
- -
- -
- -
- -
- -
c.6103+8C>T in intron 30 of CHD7: This variant is not expected to have clinical significance because it has been identified in 38.25% (9168/23972) of African ch romosomes including 1772 homozygotes by the genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs3763592). ACMG/AMP criteria applied: BA1. -
- -
- -
- -
not provided Benign:3
This variant is associated with the following publications: (PMID: 22033296, 27884173, 16400610, 21158681) -
- -
- -
CHARGE syndrome Benign:1
- -
Hypogonadotropic hypogonadism 5 with or without anosmia Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at