rs748282026

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_017780.4(CHD7):​c.2614-15_2614-14del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,136,274 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000017 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CHD7
NM_017780.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.242
Variant links:
Genes affected
CHD7 (HGNC:20626): (chromodomain helicase DNA binding protein 7) This gene encodes a protein that contains several helicase family domains. Mutations in this gene have been found in some patients with the CHARGE syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 19 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHD7NM_017780.4 linkuse as main transcriptc.2614-15_2614-14del intron_variant ENST00000423902.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHD7ENST00000423902.7 linkuse as main transcriptc.2614-15_2614-14del intron_variant 5 NM_017780.4 P1Q9P2D1-1
CHD7ENST00000524602.5 linkuse as main transcriptc.1716+38942_1716+38943del intron_variant 1 Q9P2D1-4
CHD7ENST00000525508.1 linkuse as main transcriptc.2614-15_2614-14del intron_variant 5 Q9P2D1-2
CHD7ENST00000695853.1 linkuse as main transcriptc.2614-15_2614-14del intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
150338
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000167
AC:
19
AN:
1136274
Hom.:
0
AF XY:
0.0000212
AC XY:
12
AN XY:
566840
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000294
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000232
Gnomad4 NFE exome
AF:
0.0000186
Gnomad4 OTH exome
AF:
0.0000208
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
150338
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
73288
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs748282026; hg19: chr8-61732542; API