dbSNP rs4411532: COX10-DT:n.622-56814C>T (chr17-13949656-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000582752.7(COX10-DT):n.622-56814C>T variant causes a intron 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.446

Publications

3 publications found

Variant links:

Genes affected

COX10-DT (HGNC:38873): (COX10 divergent transcript)

COX10-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
COX10-DT	ENST00000582752.7 link	n.622-56814C>T	intron_variant	Intron 2 of 4	3
COX10-DT	ENST00000602539.3 link	n.685-56817C>T	intron_variant	Intron 2 of 4	2
COX10-DT	ENST00000602743.1 link	n.225-50924C>T	intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83839

AN:

151902

Hom.:

26318

Cov.:

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.:

AF XY:

0.546

AC XY:

40526

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.251

AC:

10425

AN:

41470

American (AMR)

AF:

0.546

AC:

8347

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.648

AC:

2246

AN:

3466

East Asian (EAS)

AF:

0.412

AC:

2122

AN:

5156

South Asian (SAS)

AF:

0.659

AC:

3164

AN:

4804

European-Finnish (FIN)

AF:

0.589

AC:

6210

AN:

10542

Middle Eastern (MID)

AF:

0.620

AC:

181

AN:

292

European-Non Finnish (NFE)

AF:

0.725

AC:

49282

AN:

67984

Other (OTH)

AF:

0.587

AC:

1240

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1654

3307

4961

6614

8268

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.592

Hom.:

8197

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

(source)

DANN

Benign

0.67

PhyloP100

0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over