rs2421141

chr10-122890920-A-G

Variant summary

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

The NR_027282.1(C10orf88B):n.1190+2197A>G 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 0.474 in 151,970 control chromosomes in the GnomAD database, including 17,823 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 0.47 (17823 hom., cov: 32)
• Consequence: C10orf88B NR_027282.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf88B	NR_027282.1	n.1190+2197A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C10orf88B	ENST00000368895.2	n.1096+2197A>G		intron_variant, non_coding_transcript_variant
	ENST00000425266.3	n.827+2197A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71997 AN: 151852 Hom.: 17824 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.474 AC: 72013 AN: 151970 Hom.: 17823 Cov.: 32 AF XY: 0.476 AC XY: 35355 AN XY: 74290

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.488

Alfa AF: 0.494 Hom.: 2379

Bravo AF: 0.455

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421141; hg19: chr10-124650436;