Genetic Variant C10orf88B:n.1076A>C (chr10-122898041-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000425266.3(C10orf88B):n.1076A>C 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 0.0262 in 224,204 control chromosomes in the GnomAD database, including 113 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 0.028 ( 87 hom., cov: 32)

Exomes 𝑓: 0.022 ( 26 hom. )

Consequence

C10orf88B
ENST00000425266.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Variant links:

Genes affected

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

C10orf88B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C10orf88B	NR_027282.1 link	n.1439A>C		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C10orf88B	ENST00000425266.3 link	n.1076A>C		non_coding_transcript_exon_variant	Exon 6 of 6	2
C10orf88B	ENST00000368895.2 link	n.*17A>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.0284

AC:

4319

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0462

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0220

Gnomad ASJ

AF:

0.0481

Gnomad EAS

AF:

0.0819

Gnomad SAS

AF:

0.0149

Gnomad FIN

AF:

0.00971

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0181

Gnomad OTH

AF:

0.0148

GnomAD4 exome

AF:

0.0216

AC:

1553

AN:

71984

Hom.:

Cov.:

AF XY:

0.0199

AC XY:

819

AN XY:

41112

show subpopulations

Gnomad4 AFR exome

AF:

0.0500

Gnomad4 AMR exome

AF:

0.0421

Gnomad4 ASJ exome

AF:

0.0265

Gnomad4 EAS exome

AF:

0.0902

Gnomad4 SAS exome

AF:

0.0159

Gnomad4 FIN exome

AF:

0.00945

Gnomad4 NFE exome

AF:

0.0152

Gnomad4 OTH exome

AF:

0.0195

GnomAD4 genome

AF:

0.0284

AC:

4329

AN:

152220

Hom.:

Cov.:

AF XY:

0.0290

AC XY:

2161

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0462

Gnomad4 AMR

AF:

0.0220

Gnomad4 ASJ

AF:

0.0481

Gnomad4 EAS

AF:

0.0821

Gnomad4 SAS

AF:

0.0149

Gnomad4 FIN

AF:

0.00971

Gnomad4 NFE

AF:

0.0181

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0252

Hom.:

Bravo

AF:

0.0312

Asia WGS

AF:

0.0430

AC:

148

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.13

DANN

Benign

0.79

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