Genetic Variant C10orf88:c.369-90A>G (chr10-122952116-T-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024942.4(C10orf88):c.369-90A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 562,380 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.000011 ( 0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000107

AC:

AN:

562380

Hom.:

AF XY:

0.0000102

AC XY:

AN XY:

295394

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13422

American (AMR)

AF:

0.00

AC:

AN:

18070

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14592

East Asian (EAS)

AF:

0.00

AC:

AN:

28792

South Asian (SAS)

AF:

0.00

AC:

AN:

48078

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39980

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2046

European-Non Finnish (NFE)

AF:

0.0000163

AC:

AN:

369036

Other (OTH)

AF:

0.00

AC:

AN:

28364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

(source)

DANN

Benign

0.81

PhyloP100

-1.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over