Variant chr10-122888634-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_027282.1(C10orf88B):n.1101A>G 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 0.491 in 516,728 control chromosomes in the GnomAD database, including 63,950 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 ( 17852 hom., cov: 32)

Exomes 𝑓: 0.50 ( 46098 hom. )

Consequence

C10orf88B
NR_027282.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Variant links:

Genes affected

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

C10orf88B links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

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	Protein	UniProt
C10orf88B	NR_027282.1 linkuse as main transcript	n.1101A>G		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
C10orf88B	ENST00000368895.2 linkuse as main transcript	n.1007A>G	non_coding_transcript_exon_variant	5/6
	ENST00000425266.3 linkuse as main transcript	n.738A>G	non_coding_transcript_exon_variant	5/6	2
	ENST00000701528.1 linkuse as main transcript	n.549A>G	non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes

AF:

0.474

AC:

72053

AN:

151930

Hom.:

17853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.467

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.623

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.489

GnomAD3 exomes

AF:

0.481

AC:

109561

AN:

227566

Hom.:

26887

AF XY:

0.487

AC XY:

60128

AN XY:

123366

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.396

Gnomad ASJ exome

AF:

0.493

Gnomad EAS exome

AF:

0.429

Gnomad SAS exome

AF:

0.466

Gnomad FIN exome

AF:

0.601

Gnomad NFE exome

AF:

0.523

Gnomad OTH exome

AF:

0.497

GnomAD4 exome

AF:

0.498

AC:

181643

AN:

364680

Hom.:

46098

Cov.:

AF XY:

0.499

AC XY:

103767

AN XY:

208132

show subpopulations

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.397

Gnomad4 ASJ exome

AF:

0.496

Gnomad4 EAS exome

AF:

0.423

Gnomad4 SAS exome

AF:

0.467

Gnomad4 FIN exome

AF:

0.598

Gnomad4 NFE exome

AF:

0.529

Gnomad4 OTH exome

AF:

0.503

GnomAD4 genome

AF:

0.474

AC:

72069

AN:

152048

Hom.:

17852

Cov.:

AF XY:

0.476

AC XY:

35391

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.341

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.495

Gnomad4 EAS

AF:

0.426

Gnomad4 SAS

AF:

0.459

Gnomad4 FIN

AF:

0.623

Gnomad4 NFE

AF:

0.534

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.496

Hom.:

6908

Bravo

AF:

0.455

Asia WGS

AF:

0.436

AC:

1516

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.8

DANN

Benign

0.80

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over