rs2950354

Positions:

• chr10-122888375-C-T

Variant summary

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

The NR_027282.1(C10orf88B):​n.842C>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 0.0173 in 532,854 control chromosomes in the GnomAD database, including 152 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 0.014 (31 hom., cov: 32)
  • Exomes 𝑓: 0.019 (121 hom.)
• Consequence: C10orf88B NR_027282.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf88B	NR_027282.1	n.842C>T		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C10orf88B	ENST00000368895.2	n.748C>T		non_coding_transcript_exon_variant	5/6
	ENST00000425266.3	n.479C>T		non_coding_transcript_exon_variant	5/6	2
	ENST00000701528.1	n.290C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.0142 AC: 2161 AN: 152190 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.00299

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0683

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.00990

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.00909

GnomAD3 exomes AF: 0.0195 AC: 4795 AN: 245420 Hom.: 85 AF XY: 0.0183 AC XY: 2452 AN XY: 133744

Gnomad AFR exome AF: 0.00312

Gnomad AMR exome AF: 0.0337

Gnomad ASJ exome AF: 0.000800

Gnomad EAS exome AF: 0.0625

Gnomad SAS exome AF: 0.0136

Gnomad FIN exome AF: 0.00902

Gnomad NFE exome AF: 0.0157

Gnomad OTH exome AF: 0.0151

GnomAD4 exome AF: 0.0185 AC: 7041 AN: 380542 Hom.: 121 Cov.: 0 AF XY: 0.0176 AC XY: 3811 AN XY: 216766

Gnomad4 AFR exome AF: 0.00334

Gnomad4 AMR exome AF: 0.0345

Gnomad4 ASJ exome AF: 0.00153

Gnomad4 EAS exome AF: 0.0687

Gnomad4 SAS exome AF: 0.0131

Gnomad4 FIN exome AF: 0.00960

Gnomad4 NFE exome AF: 0.0179

Gnomad4 OTH exome AF: 0.0138

GnomAD4 genome AF: 0.0142 AC: 2162 AN: 152312 Hom.: 31 Cov.: 32 AF XY: 0.0142 AC XY: 1056 AN XY: 74480

Gnomad4 AFR AF: 0.00298

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.0685

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.00990

Gnomad4 NFE AF: 0.0175

Gnomad4 OTH AF: 0.00899

Alfa AF: 0.0155 Hom.: 6

Bravo AF: 0.0148

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2950354; hg19: chr10-124647891;