10-73920478-C-T

Variant names:

• chr10-73920478-C-T
• rs2461863
• ENST00000409178.5:n.145+2155G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000409178.5(C10orf55):​n.145+2155G>A variant causes a intron 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 ENST00000409178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409178.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf55	NR_160937.1		n.145+2155G>A		intron	N/A
	C10orf55	NR_160938.1		n.145+2155G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf55	ENST00000409178.5	TSL:1	n.145+2155G>A		intron	N/A
	C10orf55	ENST00000721915.1		n.145+2155G>A		intron	N/A
	C10orf55	ENST00000721916.1		n.162+2155G>A		intron	N/A

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

African (AFR) AF: 0.568 AC: 23336 AN: 41116

American (AMR) AF: 0.487 AC: 7405 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2198 AN: 3468

East Asian (EAS) AF: 0.172 AC: 888 AN: 5150

South Asian (SAS) AF: 0.332 AC: 1597 AN: 4804

European-Finnish (FIN) AF: 0.470 AC: 4873 AN: 10360

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39853 AN: 67902

Other (OTH) AF: 0.610 AC: 1279 AN: 2098

Alfa AF: 0.573 Hom.: 94114

Bravo AF: 0.546

Asia WGS AF: 0.258 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.41
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2461863;

hg19: chr10-75680236;