rs9804347

Positions:

• chr10-122952116-T-A
• chr10-122952116-T-C
• chr10-122952116-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
C10orf88	NM_024942.4	c.369-90A>T		intron_variant		ENST00000481909.2	NP_079218.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf88	ENST00000481909.2	c.369-90A>T		intron_variant		1	NM_024942.4	ENSP00000419126.1
C10orf88	ENST00000368891.9	n.498-90A>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69142 AN: 151874 Hom.: 16107 Cov.: 32

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

Gnomad4 AFR exome AF: 0.388

Gnomad4 AMR exome AF: 0.418

Gnomad4 ASJ exome AF: 0.394

Gnomad4 EAS exome AF: 0.533

Gnomad4 SAS exome AF: 0.476

Gnomad4 FIN exome AF: 0.574

Gnomad4 NFE exome AF: 0.479

Gnomad4 OTH exome AF: 0.459

GnomAD4 genome AF: 0.455 AC: 69144 AN: 151994 Hom.: 16100 Cov.: 32 AF XY: 0.457 AC XY: 33948 AN XY: 74310

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.451

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
DANN	Benign	0.79

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

LitVar

Other links and lift over

dbSNP: rs9804347; hg19: chr10-124711632;