Genetic Variant C10orf88B:n.1007A>G (chr10-122888634-A-G) – 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.791A>G 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 0.491 in 516,728 control chromosomes in the GnomAD database, including 63,950 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 0.47 ( 17852 hom., cov: 32)

Exomes 𝑓: 0.50 ( 46098 hom. )

Consequence

ENSG00000293310
ENST00000425266.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

8 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=-0.76).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 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.1101A>G		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
C10orf88B	ENST00000368895.2	TSL:6	n.1007A>G	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000425266.4	TSL:2	n.791A>G	non_coding_transcript_exon	Exon 5 of 6
ENSG00000293310	ENST00000701528.1		n.549A>G	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.474

AC:

72053

AN:

151930

Hom.:

17853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.467

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.623

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.489

GnomAD2 exomes

AF:

0.481

AC:

109561

AN:

227566

AF XY:

0.487

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.396

Gnomad ASJ exome

AF:

0.493

Gnomad EAS exome

AF:

0.429

Gnomad FIN exome

AF:

0.601

Gnomad NFE exome

AF:

0.523

Gnomad OTH exome

AF:

0.497

GnomAD4 exome

AF:

0.498

AC:

181643

AN:

364680

Hom.:

46098

Cov.:

AF XY:

0.499

AC XY:

103767

AN XY:

208132

show subpopulations

African (AFR)

AF:

0.340

AC:

3443

AN:

10134

American (AMR)

AF:

0.397

AC:

13884

AN:

34968

Ashkenazi Jewish (ASJ)

AF:

0.496

AC:

5729

AN:

11544

East Asian (EAS)

AF:

0.423

AC:

5343

AN:

12634

South Asian (SAS)

AF:

0.467

AC:

30574

AN:

65536

European-Finnish (FIN)

AF:

0.598

AC:

15291

AN:

25560

Middle Eastern (MID)

AF:

0.436

AC:

1241

AN:

2844

European-Non Finnish (NFE)

AF:

0.529

AC:

97993

AN:

185268

Other (OTH)

AF:

0.503

AC:

8145

AN:

16192

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

4481

8963

13444

17926

22407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

672

1344

2016

2688

3360

<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:

0.474

AC:

72069

AN:

152048

Hom.:

17852

Cov.:

AF XY:

0.476

AC XY:

35391

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.341

AC:

14141

AN:

41476

American (AMR)

AF:

0.467

AC:

7131

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.495

AC:

1715

AN:

3468

East Asian (EAS)

AF:

0.426

AC:

2201

AN:

5166

South Asian (SAS)

AF:

0.459

AC:

2213

AN:

4826

European-Finnish (FIN)

AF:

0.623

AC:

6592

AN:

10578

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.534

AC:

36268

AN:

67946

Other (OTH)

AF:

0.488

AC:

1030

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1910

3819

5729

7638

9548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.496

Hom.:

8367

Bravo

AF:

0.455

Asia WGS

AF:

0.436

AC:

1516

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.8

(source)

DANN

Benign

0.80

PhyloP100

-1.1

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