rs1891113

Variant names:

• chr10-122888081-C-T
• rs1891113
• ENST00000368895.2:n.642-188C>T

Variant summary

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

The ENST00000368895.2(C10orf88B):​n.642-188C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 152,170 control chromosomes in the GnomAD database, including 48 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: 32)
• Consequence: C10orf88B ENST00000368895.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368895.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	NR_027282.1		n.736-188C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	ENST00000368895.2	TSL:6	n.642-188C>T		intron	N/A
	ENSG00000293310	ENST00000425266.4	TSL:2	n.426-188C>T		intron	N/A
	ENSG00000293310	ENST00000701528.1		n.184-188C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3230 AN: 152052 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0198

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.0808

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00973

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0213 AC: 3241 AN: 152170 Hom.: 48 Cov.: 32 AF XY: 0.0216 AC XY: 1608 AN XY: 74382

African (AFR) AF: 0.0213 AC: 883 AN: 41510

American (AMR) AF: 0.0198 AC: 303 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3470

East Asian (EAS) AF: 0.0810 AC: 419 AN: 5176

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4818

European-Finnish (FIN) AF: 0.00973 AC: 103 AN: 10586

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

European-Non Finnish (NFE) AF: 0.0180 AC: 1227 AN: 68014

Other (OTH) AF: 0.0137 AC: 29 AN: 2114

Alfa AF: 0.0212 Hom.: 4

Bravo AF: 0.0230

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.60
PhyloP100		0.062
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: rs1891113; hg19: chr10-124647597;