Genetic Variant C10orf88B:n.748C>T (chr10-122888375-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000425266.4(ENSG00000293310):n.532C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 532,854 control chromosomes in the GnomAD database, including 152 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 0.014 ( 31 hom., cov: 32)

Exomes 𝑓: 0.019 ( 121 hom. )

Consequence

ENSG00000293310
ENST00000425266.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.994

Publications

3 publications found

Variant links:

Genes affected

C10orf88B (HGNC:44080): (C10orf88B (pseudogene))

C10orf88B links:

ENSG00000293310 (HGNC:):

ENSG00000293310 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=-0.61).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425266.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	NR_027282.1		n.842C>T		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
C10orf88B	ENST00000368895.2	TSL:6	n.748C>T	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000425266.4	TSL:2	n.532C>T	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000701528.1		n.290C>T	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0142

AC:

2161

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00299

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0168

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.0683

Gnomad SAS

AF:

0.0141

Gnomad FIN

AF:

0.00990

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0175

Gnomad OTH

AF:

0.00909

GnomAD2 exomes

AF:

0.0195

AC:

4795

AN:

245420

AF XY:

0.0183

show subpopulations

Gnomad AFR exome

AF:

0.00312

Gnomad AMR exome

AF:

0.0337

Gnomad ASJ exome

AF:

0.000800

Gnomad EAS exome

AF:

0.0625

Gnomad FIN exome

AF:

0.00902

Gnomad NFE exome

AF:

0.0157

Gnomad OTH exome

AF:

0.0151

GnomAD4 exome

AF:

0.0185

AC:

7041

AN:

380542

Hom.:

121

Cov.:

AF XY:

0.0176

AC XY:

3811

AN XY:

216766

show subpopulations

African (AFR)

AF:

0.00334

AC:

AN:

10482

American (AMR)

AF:

0.0345

AC:

1248

AN:

36224

Ashkenazi Jewish (ASJ)

AF:

0.00153

AC:

AN:

11738

East Asian (EAS)

AF:

0.0687

AC:

903

AN:

13140

South Asian (SAS)

AF:

0.0131

AC:

882

AN:

67362

European-Finnish (FIN)

AF:

0.00960

AC:

289

AN:

30102

Middle Eastern (MID)

AF:

0.00210

AC:

AN:

2854

European-Non Finnish (NFE)

AF:

0.0179

AC:

3430

AN:

191954

Other (OTH)

AF:

0.0138

AC:

230

AN:

16686

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.456

Heterozygous variant carriers

375

749

1124

1498

1873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

124

186

248

310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0142

AC:

2162

AN:

152312

Hom.:

Cov.:

AF XY:

0.0142

AC XY:

1056

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.00298

AC:

124

AN:

41578

American (AMR)

AF:

0.0169

AC:

258

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3472

East Asian (EAS)

AF:

0.0685

AC:

355

AN:

5184

South Asian (SAS)

AF:

0.0141

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00990

AC:

105

AN:

10608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0175

AC:

1188

AN:

68024

Other (OTH)

AF:

0.00899

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

114

229

343

458

572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<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:

0.0127

Hom.:

Bravo

AF:

0.0148

Asia WGS

AF:

0.0300

AC:

105

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

0.99

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over