10-122888634-A-G

Variant names:

• chr10-122888634-A-G
• rs10902838
• ENST00000368895.2:n.1007A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000368895.2(C10orf88B):​n.1007A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 516,728 control chromosomes in the GnomAD database, including 63,950 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 0.47 (17852 hom., cov: 32)
  • Exomes 𝑓: 0.50 (46098 hom.)
• Consequence: C10orf88B ENST00000368895.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 8 publications found

Genes affected

C10orf88B (HGNC:44080): (C10orf88B (pseudogene))

ENSG00000293310 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368895.2. 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
	C10orf88B	NR_027282.1		n.1101A>G		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	ENST00000368895.2	TSL:6	n.1007A>G		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000293310	ENST00000425266.4	TSL:2	n.791A>G		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000293310	ENST00000701528.1		n.549A>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72053 AN: 151930 Hom.: 17853 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.489

GnomAD2 exomes AF: 0.481 AC: 109561 AN: 227566 AF XY: 0.487

Gnomad AFR exome AF: 0.327

Gnomad AMR exome AF: 0.396

Gnomad ASJ exome AF: 0.493

Gnomad EAS exome AF: 0.429

Gnomad FIN exome AF: 0.601

Gnomad NFE exome AF: 0.523

Gnomad OTH exome AF: 0.497

GnomAD4 exome AF: 0.498 AC: 181643 AN: 364680 Hom.: 46098 Cov.: 0 AF XY: 0.499 AC XY: 103767 AN XY: 208132

African (AFR) AF: 0.340 AC: 3443 AN: 10134

American (AMR) AF: 0.397 AC: 13884 AN: 34968

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 5729 AN: 11544

East Asian (EAS) AF: 0.423 AC: 5343 AN: 12634

South Asian (SAS) AF: 0.467 AC: 30574 AN: 65536

European-Finnish (FIN) AF: 0.598 AC: 15291 AN: 25560

Middle Eastern (MID) AF: 0.436 AC: 1241 AN: 2844

European-Non Finnish (NFE) AF: 0.529 AC: 97993 AN: 185268

Other (OTH) AF: 0.503 AC: 8145 AN: 16192

GnomAD4 genome AF: 0.474 AC: 72069 AN: 152048 Hom.: 17852 Cov.: 32 AF XY: 0.476 AC XY: 35391 AN XY: 74328

African (AFR) AF: 0.341 AC: 14141 AN: 41476

American (AMR) AF: 0.467 AC: 7131 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1715 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2201 AN: 5166

South Asian (SAS) AF: 0.459 AC: 2213 AN: 4826

European-Finnish (FIN) AF: 0.623 AC: 6592 AN: 10578

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36268 AN: 67946

Other (OTH) AF: 0.488 AC: 1030 AN: 2112

Alfa AF: 0.496 Hom.: 8367

Bravo AF: 0.455

Asia WGS AF: 0.436 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.8
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10902838; hg19: chr10-124648150;