rs11248323

Variant names:

• chr10-122888690-C-T
• rs11248323
• ENST00000368895.2:n.1063C>T

Variant summary

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

The ENST00000368895.2(C10orf88B):​n.1063C>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 ENST00000368895.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 5 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=-0.92).
• 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 rank	MANE	Protein	UniProt
C10orf88B	NR_027282.1	n.1157C>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.1063C>T		non_coding_transcript_exon_variant	Exon 5 of 6	6
ENSG00000293310	ENST00000425266.4	n.847C>T		non_coding_transcript_exon_variant	Exon 5 of 6	2
ENSG00000293310	ENST00000701528.1	n.605C>T		non_coding_transcript_exon_variant	Exon 4 of 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

GnomAD2 exomes AF: 0.0273 AC: 5372 AN: 197050 AF XY: 0.0255

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 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

African (AFR) AF: 0.0223 AC: 204 AN: 9158

American (AMR) AF: 0.0391 AC: 1225 AN: 31364

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 418 AN: 9854

East Asian (EAS) AF: 0.0859 AC: 1064 AN: 12388

South Asian (SAS) AF: 0.0135 AC: 814 AN: 60474

European-Finnish (FIN) AF: 0.0110 AC: 211 AN: 19154

Middle Eastern (MID) AF: 0.00558 AC: 15 AN: 2688

European-Non Finnish (NFE) AF: 0.0189 AC: 3289 AN: 173984

Other (OTH) AF: 0.0200 AC: 300 AN: 15012

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

African (AFR) AF: 0.0213 AC: 885 AN: 41534

American (AMR) AF: 0.0199 AC: 304 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3470

East Asian (EAS) AF: 0.0817 AC: 422 AN: 5166

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4826

European-Finnish (FIN) AF: 0.00989 AC: 105 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0180 AC: 1227 AN: 68024

Other (OTH) AF: 0.0137 AC: 29 AN: 2110

Alfa AF: 0.0215 Hom.: 14

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11248323; hg19: chr10-124648206;