2-232531264-GGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT-GGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCTGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000751.3(CHRND):​c.821-52_821-18dupGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000892 in 953,304 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 0.00012 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000084 ( 0 hom. )

Consequence

CHRND
NM_000751.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.301
Variant links:
Genes affected
CHRND (HGNC:1965): (cholinergic receptor nicotinic delta subunit) The acetylcholine receptor of muscle has 5 subunits of 4 different types: 2 alpha and 1 each of beta, gamma and delta subunits. After acetylcholine binding, the receptor undergoes an extensive conformation change that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. Defects in this gene are a cause of multiple pterygium syndrome lethal type (MUPSL), congenital myasthenic syndrome slow-channel type (SCCMS), and congenital myasthenic syndrome fast-channel type (FCCMS). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHRNDNM_000751.3 linkc.821-52_821-18dupGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT intron_variant ENST00000258385.8 NP_000742.1 Q07001-1
CHRNDNM_001256657.2 linkc.776-52_776-18dupGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT intron_variant NP_001243586.1 Q07001-2
CHRNDNM_001311196.2 linkc.518-52_518-18dupGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT intron_variant NP_001298125.1 Q07001
CHRNDNM_001311195.2 linkc.239-52_239-18dupGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT intron_variant NP_001298124.1 Q07001B4E3W4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHRNDENST00000258385.8 linkc.821-88_821-87insGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCT intron_variant 1 NM_000751.3 ENSP00000258385.3 Q07001-1

Frequencies

GnomAD3 genomes
AF:
0.000119
AC:
18
AN:
151586
Hom.:
0
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.0000728
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000394
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000209
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000836
AC:
67
AN:
801718
Hom.:
0
AF XY:
0.0000969
AC XY:
41
AN XY:
423314
show subpopulations
Gnomad4 AFR exome
AF:
0.0000467
Gnomad4 AMR exome
AF:
0.0000235
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000166
Gnomad4 SAS exome
AF:
0.000222
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000798
Gnomad4 OTH exome
AF:
0.0000519
GnomAD4 genome
AF:
0.000119
AC:
18
AN:
151586
Hom.:
0
Cov.:
28
AF XY:
0.000135
AC XY:
10
AN XY:
73992
show subpopulations
Gnomad4 AFR
AF:
0.0000728
Gnomad4 AMR
AF:
0.000394
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000209
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs530117757; hg19: chr2-233395974; API