rs10493275

Positions:

• chr1-59990125-A-G
• chr1-59990125-A-T

Variant summary

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

The ENST00000486478.5(C1orf87):​n.1202T>C 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 0.0938 in 152,262 control chromosomes in the GnomAD database, including 738 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 0.094 (738 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: C1orf87 ENST00000486478.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669

Genes affected

C1orf87 (HGNC:28547): (chromosome 1 open reading frame 87)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf87	ENST00000486478.5	n.1202T>C		non_coding_transcript_exon_variant	4/6	2

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14282 AN: 152144 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.0927

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 42 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 26

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0938 AC: 14275 AN: 152262 Hom.: 738 Cov.: 32 AF XY: 0.0946 AC XY: 7043 AN XY: 74454

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0748 Hom.: 496

Bravo AF: 0.0958

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493275; hg19: chr1-60455797;