rs2461863

chr10-73920478-C-T

Variant summary

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

The NR_160938.1(C10orf55):n.145+2155G>A 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 0.543 in 151,296 control chromosomes in the GnomAD database, including 23,010 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 0.54 (23010 hom., cov: 29)
• Consequence: C10orf55 NR_160938.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898

Genes affected

C10orf55 (HGNC:31008): (chromosome 10 putative open reading frame 55) Enables identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf55	NR_160938.1	n.145+2155G>A		intron_variant, non_coding_transcript_variant
C10orf55	NR_160937.1	n.145+2155G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C10orf55	ENST00000409178.5	n.145+2155G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82032 AN: 151176 Hom.: 22994 Cov.: 29

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.543 AC: 82084 AN: 151296 Hom.: 23010 Cov.: 29 AF XY: 0.534 AC XY: 39392 AN XY: 73836

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.610

Alfa AF: 0.584 Hom.: 44174

Bravo AF: 0.546

Asia WGS AF: 0.258 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.65
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2461863; hg19: chr10-75680236;