rs11248323

Positions:

• chr10-122888690-C-T

Variant summary

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

The ENST00000425266.3(C10orf88B):​n.794C>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 0.0222 in 486,320 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 (48 hom., cov: 33)
  • Exomes 𝑓: 0.023 (138 hom.)
• Consequence: C10orf88B ENST00000425266.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

C10orf88B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf88B	NR_027282.1	n.1157C>T		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf88B	ENST00000368895.2	n.1063C>T		non_coding_transcript_exon_variant	5/6	6
C10orf88B	ENST00000425266.3	n.794C>T		non_coding_transcript_exon_variant	5/6	2
C10orf88B	ENST00000701528.1	n.605C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3237 AN: 152126 Hom.: 48 Cov.: 33

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0198

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0815

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0125

GnomAD3 exomes AF: 0.0273 AC: 5372 AN: 197050 Hom.: 116 AF XY: 0.0255 AC XY: 2722 AN XY: 106878

Gnomad AFR exome AF: 0.0230

Gnomad AMR exome AF: 0.0381

Gnomad ASJ exome AF: 0.0459

Gnomad EAS exome AF: 0.0822

Gnomad SAS exome AF: 0.0154

Gnomad FIN exome AF: 0.0111

Gnomad NFE exome AF: 0.0183

Gnomad OTH exome AF: 0.0234

GnomAD4 exome AF: 0.0226 AC: 7540 AN: 334076 Hom.: 138 Cov.: 0 AF XY: 0.0213 AC XY: 4060 AN XY: 191048

Gnomad4 AFR exome AF: 0.0223

Gnomad4 AMR exome AF: 0.0391

Gnomad4 ASJ exome AF: 0.0424

Gnomad4 EAS exome AF: 0.0859

Gnomad4 SAS exome AF: 0.0135

Gnomad4 FIN exome AF: 0.0110

Gnomad4 NFE exome AF: 0.0189

Gnomad4 OTH exome AF: 0.0200

GnomAD4 genome AF: 0.0213 AC: 3248 AN: 152244 Hom.: 48 Cov.: 33 AF XY: 0.0217 AC XY: 1614 AN XY: 74450

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0199

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0817

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.00989

Gnomad4 NFE AF: 0.0180

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0217 Hom.: 12

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	-0.92
CADD	Benign	0.17
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11248323; hg19: chr10-124648206;