chr10-122887918-C-T

Variant names:

• chr10-122887918-C-T
• rs2950355
• ENST00000368895.2:n.642-351C>T

Variant summary

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

The ENST00000368895.2(C10orf88B):​n.642-351C>T variant causes a intron 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 ENST00000368895.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 2 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=-0.99).
• 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 rank	MANE	Protein	UniProt
C10orf88B	NR_027282.1	n.736-351C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C10orf88B	ENST00000368895.2	n.642-351C>T		intron_variant	Intron 4 of 5	6
ENSG00000293310	ENST00000425266.4	n.426-351C>T		intron_variant	Intron 4 of 5	2
ENSG00000293310	ENST00000701528.1	n.184-351C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.0246 AC: 1022 AN: 41498

American (AMR) AF: 0.0200 AC: 305 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3468

East Asian (EAS) AF: 0.0814 AC: 422 AN: 5184

South Asian (SAS) AF: 0.0154 AC: 74 AN: 4816

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10580

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1232 AN: 67998

Other (OTH) AF: 0.0151 AC: 32 AN: 2114

Alfa AF: 0.0211 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
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2950355; hg19: chr10-124647434;