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rs56145914

chr1-6640071-CAAAAAA-Cchr1-6640071-CAAAAAA-CAAchr1-6640071-CAAAAAA-CAAAchr1-6640071-CAAAAAA-CAAAAchr1-6640071-CAAAAAA-CAAAAAchr1-6640071-CAAAAAA-CAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAAAAAAAchr1-6640071-CAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018198.4(DNAJC11):c.1098-20_1098-15del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000246 in 1,219,026 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 0.000012 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000018 ( 0 hom. )

Consequence

DNAJC11
NM_018198.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23
Variant links:
Genes affected
DNAJC11 (HGNC:25570): (DnaJ heat shock protein family (Hsp40) member C11) Involved in cristae formation. Located in mitochondrial outer membrane and nuclear speck. Part of MIB complex. Colocalizes with MICOS complex and SAM complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DNAJC11NM_018198.4 linkuse as main transcriptc.1098-20_1098-15del splice_polypyrimidine_tract_variant, intron_variant ENST00000377577.10
DNAJC11XM_047424842.1 linkuse as main transcriptc.828-20_828-15del splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DNAJC11ENST00000377577.10 linkuse as main transcriptc.1098-20_1098-15del splice_polypyrimidine_tract_variant, intron_variant 1 NM_018198.4 P1Q9NVH1-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000121
AC:
1
AN:
82518
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000500
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:
0.00000176
AC:
2
AN:
1136508
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
548480
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000215
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000121
AC:
1
AN:
82518
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
38372
show subpopulations
Gnomad4 AFR
AF:
0.0000500
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

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: rs56145914; hg19: chr1-6700131; API