dbSNP rs9423288: C10orf88B:n.830C>T (chr10-122888457-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.614C>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 0.0215 in 517,380 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 ( 45 hom., cov: 32)

Exomes 𝑓: 0.022 ( 141 hom. )

Consequence

ENSG00000293310
ENST00000425266.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0738 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.924C>T		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
C10orf88B	ENST00000368895.2	TSL:6	n.830C>T	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000425266.4	TSL:2	n.614C>T	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000701528.1		n.372C>T	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0212

AC:

3228

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0211

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0200

Gnomad ASJ

AF:

0.0484

Gnomad EAS

AF:

0.0800

Gnomad SAS

AF:

0.0149

Gnomad FIN

AF:

0.00990

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0180

Gnomad OTH

AF:

0.0124

GnomAD2 exomes

AF:

0.0250

AC:

5522

AN:

220474

AF XY:

0.0235

show subpopulations

Gnomad AFR exome

AF:

0.0218

Gnomad AMR exome

AF:

0.0366

Gnomad ASJ exome

AF:

0.0428

Gnomad EAS exome

AF:

0.0797

Gnomad FIN exome

AF:

0.00922

Gnomad NFE exome

AF:

0.0173

Gnomad OTH exome

AF:

0.0212

GnomAD4 exome

AF:

0.0216

AC:

7905

AN:

365140

Hom.:

141

Cov.:

AF XY:

0.0206

AC XY:

4289

AN XY:

208078

show subpopulations

African (AFR)

AF:

0.0206

AC:

201

AN:

9776

American (AMR)

AF:

0.0374

AC:

1292

AN:

34506

Ashkenazi Jewish (ASJ)

AF:

0.0415

AC:

480

AN:

11576

East Asian (EAS)

AF:

0.0837

AC:

1002

AN:

11972

South Asian (SAS)

AF:

0.0135

AC:

881

AN:

65432

European-Finnish (FIN)

AF:

0.00982

AC:

287

AN:

29226

Middle Eastern (MID)

AF:

0.00564

AC:

AN:

2838

European-Non Finnish (NFE)

AF:

0.0187

AC:

3439

AN:

183728

Other (OTH)

AF:

0.0191

AC:

307

AN:

16086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

387

775

1162

1550

1937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

136

204

272

340

<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:

3239

AN:

152240

Hom.:

Cov.:

AF XY:

0.0216

AC XY:

1611

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0212

AC:

882

AN:

41540

American (AMR)

AF:

0.0200

AC:

306

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0484

AC:

168

AN:

3472

East Asian (EAS)

AF:

0.0801

AC:

414

AN:

5166

South Asian (SAS)

AF:

0.0149

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00990

AC:

105

AN:

10608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0180

AC:

1225

AN:

68024

Other (OTH)

AF:

0.0137

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

165

331

496

662

827

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:

0.0219

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

-0.89

CADD

Benign

0.32

(source)

DANN

Benign

0.66

PhyloP100

-0.41

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