rs4403744

Positions:

• chr10-122898482-G-A
• chr10-122898482-G-T

Variant summary

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

The NR_027282.1(C10orf88B):​n.1880G>A 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 151,902 control chromosomes in the GnomAD database, including 18,814 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 0.49 (18814 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: C10orf88B NR_027282.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf88B	NR_027282.1	n.1880G>A		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000425266.3	n.1517G>A		non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74529 AN: 151784 Hom.: 18815 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.495

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.491 AC: 74543 AN: 151902 Hom.: 18814 Cov.: 31 AF XY: 0.492 AC XY: 36526 AN XY: 74236

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.493

Alfa AF: 0.504 Hom.: 2607

Bravo AF: 0.473

Asia WGS AF: 0.436 AC: 1515 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.6
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4403744; hg19: chr10-124657998;