chr10-122952116-T-A

Variant names:

• chr10-122952116-T-A
• rs9804347
• NM_024942.4:c.369-90A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024942.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88	NM_024942.4	MANE Select	c.369-90A>T		intron	N/A	NP_079218.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88	ENST00000481909.2	TSL:1 MANE Select	c.369-90A>T		intron	N/A	ENSP00000419126.1
	C10orf88	ENST00000368891.9	TSL:2	n.498-90A>T		intron	N/A
	C10orf88	ENST00000470158.1	TSL:3	n.-109A>T		upstream_gene	N/A

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

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

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

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.77
DANN	Benign	0.79
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9804347; hg19: chr10-124711632;