rs6599638

Positions:

• chr10-122944633-G-A
• chr10-122944633-G-C
• chr10-122944633-G-T

Variant summary

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

The NM_024942.4(C10orf88):​c.648+4016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,870 control chromosomes in the GnomAD database, including 16,070 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 (16070 hom., cov: 30)
• Consequence: C10orf88 NM_024942.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf88	NM_024942.4	c.648+4016C>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.648+4016C>T		intron_variant		1	NM_024942.4	ENSP00000419126	P1
C10orf88	ENST00000368891.9	n.777+4016C>T		intron_variant, non_coding_transcript_variant		2
C10orf88	ENST00000470158.1	n.161+4016C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69053 AN: 151750 Hom.: 16077 Cov.: 30

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.453

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.455 AC: 69055 AN: 151870 Hom.: 16070 Cov.: 30 AF XY: 0.457 AC XY: 33902 AN XY: 74216

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.451

Alfa AF: 0.465 Hom.: 33088

Bravo AF: 0.439

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.30

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: rs6599638; hg19: chr10-124704149;