rs2227578

Variant names:

• chr10-73918957-G-A
• rs2227578
• ENST00000409178.5:n.146-2316C>T

Variant summary

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

The ENST00000409178.5(C10orf55):​n.146-2316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,956 control chromosomes in the GnomAD database, including 19,228 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 (19228 hom., cov: 30)
• Consequence: C10orf55 ENST00000409178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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.146-2316C>T		intron	N/A
	C10orf55	NR_160938.1		n.146-2316C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf55	ENST00000409178.5	TSL:1	n.146-2316C>T		intron	N/A
	C10orf55	ENST00000721915.1		n.146-2316C>T		intron	N/A
	C10orf55	ENST00000721916.1		n.162+3676C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74947 AN: 151838 Hom.: 19225 Cov.: 30

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.493 AC: 74968 AN: 151956 Hom.: 19228 Cov.: 30 AF XY: 0.486 AC XY: 36067 AN XY: 74220

African (AFR) AF: 0.448 AC: 18562 AN: 41434

American (AMR) AF: 0.462 AC: 7048 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2036 AN: 3470

East Asian (EAS) AF: 0.118 AC: 612 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4818

European-Finnish (FIN) AF: 0.465 AC: 4897 AN: 10534

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38586 AN: 67944

Other (OTH) AF: 0.557 AC: 1177 AN: 2112

Alfa AF: 0.496 Hom.: 3215

Bravo AF: 0.494

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.43
PhyloP100		0.71
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: rs2227578;

hg19: chr10-75678715;