rs9423288

Variant names:

• chr10-122888457-C-T
• rs9423288
• ENST00000368895.2:n.830C>T

Variant summary

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

The ENST00000425266.3(C10orf88B):​n.561C>T 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 0.0215 in 517,380 control chromosomes in the GnomAD database, including 186 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 0.021 (45 hom., cov: 32)
  • Exomes 𝑓: 0.022 (141 hom.)
• Consequence: C10orf88B ENST00000425266.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C10orf88B	NR_027282.1	n.924C>T		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C10orf88B	ENST00000368895.2	n.830C>T		non_coding_transcript_exon_variant	Exon 5 of 6	6
C10orf88B	ENST00000425266.3	n.561C>T		non_coding_transcript_exon_variant	Exon 5 of 6	2
C10orf88B	ENST00000701528.1	n.372C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3228 AN: 152122 Hom.: 45 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.00990

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0124

GnomAD3 exomes AF: 0.0250 AC: 5522 AN: 220474 Hom.: 115 AF XY: 0.0235 AC XY: 2815 AN XY: 119842

Gnomad AFR exome AF: 0.0218

Gnomad AMR exome AF: 0.0366

Gnomad ASJ exome AF: 0.0428

Gnomad EAS exome AF: 0.0797

Gnomad SAS exome AF: 0.0144

Gnomad FIN exome AF: 0.00922

Gnomad NFE exome AF: 0.0173

Gnomad OTH exome AF: 0.0212

GnomAD4 exome AF: 0.0216 AC: 7905 AN: 365140 Hom.: 141 Cov.: 0 AF XY: 0.0206 AC XY: 4289 AN XY: 208078

Gnomad4 AFR exome AF: 0.0206

Gnomad4 AMR exome AF: 0.0374

Gnomad4 ASJ exome AF: 0.0415

Gnomad4 EAS exome AF: 0.0837

Gnomad4 SAS exome AF: 0.0135

Gnomad4 FIN exome AF: 0.00982

Gnomad4 NFE exome AF: 0.0187

Gnomad4 OTH exome AF: 0.0191

GnomAD4 genome AF: 0.0213 AC: 3239 AN: 152240 Hom.: 45 Cov.: 32 AF XY: 0.0216 AC XY: 1611 AN XY: 74440

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.0801

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.00990

Gnomad4 NFE AF: 0.0180

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0217 Hom.: 10

Bravo AF: 0.0230

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9423288; hg19: chr10-124647973;