rs2950355

Positions:

• chr10-122887918-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.736-351C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 152,142 control chromosomes in the GnomAD database, including 55 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 0.022 (55 hom., cov: 32)
• Consequence: C10orf88B NR_027282.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.075 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf88B	NR_027282.1	n.736-351C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf88B	ENST00000368895.2	n.642-351C>T		intron_variant, non_coding_transcript_variant
	ENST00000425266.3	n.373-351C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000701528.1	n.184-351C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3389 AN: 152022 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.0154

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0223 AC: 3400 AN: 152142 Hom.: 55 Cov.: 32 AF XY: 0.0226 AC XY: 1684 AN XY: 74370

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.0814

Gnomad4 SAS AF: 0.0154

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0181

Gnomad4 OTH AF: 0.0151

Alfa AF: 0.0209 Hom.: 9

Bravo AF: 0.0240

Asia WGS AF: 0.0410 AC: 141 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2950355; hg19: chr10-124647434;