rs4411532

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000582752.7(COX10-DT):​n.622-56814C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,014 control chromosomes in the GnomAD database, including 26,315 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.55 ( 26315 hom., cov: 32)

Consequence

COX10-DT
ENST00000582752.7 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.446
Variant links:
Genes affected
COX10-DT (HGNC:38873): (COX10 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COX10-DTENST00000582752.7 linkuse as main transcriptn.622-56814C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.552
AC:
83839
AN:
151902
Hom.:
26318
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.252
Gnomad AMI
AF:
0.703
Gnomad AMR
AF:
0.547
Gnomad ASJ
AF:
0.648
Gnomad EAS
AF:
0.411
Gnomad SAS
AF:
0.657
Gnomad FIN
AF:
0.589
Gnomad MID
AF:
0.627
Gnomad NFE
AF:
0.725
Gnomad OTH
AF:
0.588
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.552
AC:
83855
AN:
152014
Hom.:
26315
Cov.:
32
AF XY:
0.546
AC XY:
40526
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.251
Gnomad4 AMR
AF:
0.546
Gnomad4 ASJ
AF:
0.648
Gnomad4 EAS
AF:
0.412
Gnomad4 SAS
AF:
0.659
Gnomad4 FIN
AF:
0.589
Gnomad4 NFE
AF:
0.725
Gnomad4 OTH
AF:
0.587
Alfa
AF:
0.598
Hom.:
8167
Bravo
AF:
0.532
Asia WGS
AF:
0.506
AC:
1761
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.91
DANN
Benign
0.67

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: rs4411532; hg19: chr17-13852973; API