dbSNP rs11248323: C10orf88B:n.1063C>T (chr10-122888690-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.847C>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 0.0222 in 486,320 control chromosomes in the GnomAD database, including 186 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 0.021 ( 48 hom., cov: 33)

Exomes 𝑓: 0.023 ( 138 hom. )

Consequence

ENSG00000293310
ENST00000425266.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

Publications

5 publications found

Variant links:

Genes affected

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

C10orf88B links:

ENSG00000293310 (HGNC:):

ENSG00000293310 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000425266.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0753 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.1157C>T		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
C10orf88B	ENST00000368895.2	TSL:6	n.1063C>T	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000425266.4	TSL:2	n.847C>T	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000701528.1		n.605C>T	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0213

AC:

3237

AN:

152126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0212

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0198

Gnomad ASJ

AF:

0.0481

Gnomad EAS

AF:

0.0815

Gnomad SAS

AF:

0.0147

Gnomad FIN

AF:

0.00989

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.0180

Gnomad OTH

AF:

0.0125

GnomAD2 exomes

AF:

0.0273

AC:

5372

AN:

197050

AF XY:

0.0255

show subpopulations

Gnomad AFR exome

AF:

0.0230

Gnomad AMR exome

AF:

0.0381

Gnomad ASJ exome

AF:

0.0459

Gnomad EAS exome

AF:

0.0822

Gnomad FIN exome

AF:

0.0111

Gnomad NFE exome

AF:

0.0183

Gnomad OTH exome

AF:

0.0234

GnomAD4 exome

AF:

0.0226

AC:

7540

AN:

334076

Hom.:

138

Cov.:

AF XY:

0.0213

AC XY:

4060

AN XY:

191048

show subpopulations

African (AFR)

AF:

0.0223

AC:

204

AN:

9158

American (AMR)

AF:

0.0391

AC:

1225

AN:

31364

Ashkenazi Jewish (ASJ)

AF:

0.0424

AC:

418

AN:

9854

East Asian (EAS)

AF:

0.0859

AC:

1064

AN:

12388

South Asian (SAS)

AF:

0.0135

AC:

814

AN:

60474

European-Finnish (FIN)

AF:

0.0110

AC:

211

AN:

19154

Middle Eastern (MID)

AF:

0.00558

AC:

AN:

2688

European-Non Finnish (NFE)

AF:

0.0189

AC:

3289

AN:

173984

Other (OTH)

AF:

0.0200

AC:

300

AN:

15012

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

350

700

1051

1401

1751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

210

280

350

<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:

0.0213

AC:

3248

AN:

152244

Hom.:

Cov.:

AF XY:

0.0217

AC XY:

1614

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0213

AC:

885

AN:

41534

American (AMR)

AF:

0.0199

AC:

304

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0481

AC:

167

AN:

3470

East Asian (EAS)

AF:

0.0817

AC:

422

AN:

5166

South Asian (SAS)

AF:

0.0147

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00989

AC:

105

AN:

10612

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0180

AC:

1227

AN:

68024

Other (OTH)

AF:

0.0137

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

158

316

474

632

790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<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:

0.0215

Hom.:

Bravo

AF:

0.0230

Asia WGS

AF:

0.0400

AC:

139

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.17

(source)

DANN

Benign

0.64

PhyloP100

-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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