Genetic Variant NM_024942.4:c.369-90A>T (chr10-122952116-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024942.4(C10orf88):c.369-90A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 712,582 control chromosomes in the GnomAD database, including 81,845 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 0.45 ( 16100 hom., cov: 32)

Exomes 𝑓: 0.48 ( 65745 hom. )

Consequence

C10orf88
NM_024942.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

1 publications found

Variant links:

Genes affected

C10orf88 (HGNC:25822): (chromosome 10 open reading frame 88) Predicted to enable identical protein binding activity. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

C10orf88 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C10orf88	NM_024942.4 link	c.369-90A>T		intron_variant	Intron 2 of 5	ENST00000481909.2	NP_079218.2	Q9H8K7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
C10orf88	ENST00000481909.2 link	c.369-90A>T	intron_variant	Intron 2 of 5	1	NM_024942.4	ENSP00000419126.1	Q9H8K7
C10orf88	ENST00000368891.9 link	n.498-90A>T	intron_variant	Intron 2 of 5	2
C10orf88	ENST00000470158.1 link	n.-109A>T	upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.455

AC:

69142

AN:

151874

Hom.:

16107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.382

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.521

Gnomad SAS

AF:

0.479

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.423

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.453

GnomAD4 exome

AF:

0.481

AC:

269367

AN:

560588

Hom.:

65745

AF XY:

0.480

AC XY:

141264

AN XY:

294478

show subpopulations

African (AFR)

AF:

0.388

AC:

5191

AN:

13390

American (AMR)

AF:

0.418

AC:

7515

AN:

17970

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

5726

AN:

14544

East Asian (EAS)

AF:

0.533

AC:

15289

AN:

28672

South Asian (SAS)

AF:

0.476

AC:

22835

AN:

47956

European-Finnish (FIN)

AF:

0.574

AC:

22909

AN:

39896

Middle Eastern (MID)

AF:

0.420

AC:

856

AN:

2036

European-Non Finnish (NFE)

AF:

0.479

AC:

176080

AN:

367860

Other (OTH)

AF:

0.459

AC:

12966

AN:

28264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

6616

13232

19848

26464

33080

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2590

5180

7770

10360

12950

<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:

0.455

AC:

69144

AN:

151994

Hom.:

16100

Cov.:

AF XY:

0.457

AC XY:

33948

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.381

AC:

15794

AN:

41452

American (AMR)

AF:

0.428

AC:

6543

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1379

AN:

3464

East Asian (EAS)

AF:

0.523

AC:

2708

AN:

5180

South Asian (SAS)

AF:

0.479

AC:

2311

AN:

4828

European-Finnish (FIN)

AF:

0.576

AC:

6071

AN:

10542

Middle Eastern (MID)

AF:

0.421

AC:

123

AN:

292

European-Non Finnish (NFE)

AF:

0.481

AC:

32649

AN:

67942

Other (OTH)

AF:

0.451

AC:

952

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1925

3850

5775

7700

9625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

644

1288

1932

2576

3220

<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:

0.470

Hom.:

2149

Bravo

AF:

0.439

Asia WGS

AF:

0.482

AC:

1674

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.77

(source)

DANN

Benign

0.79

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over