rs10494266

Positions:

• chr1-150273149-A-G

Variant summary

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

The NM_024579.4(C1orf54):​c.46+286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,206 control chromosomes in the GnomAD database, including 1,343 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 0.12 (1343 hom., cov: 32)
• Consequence: C1orf54 NM_024579.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

C1orf54 (HGNC:26258): (chromosome 1 open reading frame 54) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904414 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf54	NM_024579.4	c.46+286A>G		intron_variant		ENST00000369099.8	NP_078855.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf54	ENST00000369099.8	c.46+286A>G		intron_variant		1	NM_024579.4	ENSP00000358095.3
C1orf54	ENST00000369098.3	c.46+286A>G		intron_variant		1		ENSP00000358094.3
C1orf54	ENST00000369102.5	c.46+286A>G		intron_variant		5		ENSP00000358098.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18137 AN: 152090 Hom.: 1344 Cov.: 32

Gnomad AFR AF: 0.0596

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.119 AC: 18135 AN: 152206 Hom.: 1343 Cov.: 32 AF XY: 0.124 AC XY: 9258 AN XY: 74416

Gnomad4 AFR AF: 0.0597

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.147

Alfa AF: 0.127 Hom.: 1397

Bravo AF: 0.115

Asia WGS AF: 0.244 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494266; hg19: chr1-150245552;