rs10493275

Variant names:

• chr1-59990125-A-G
• rs10493275
• ENST00000486478.5:n.1202T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf87	ENST00000486478.5	n.1202T>C		non_coding_transcript_exon_variant	Exon 4 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 34

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.120 AC: 4964 AN: 41532

American (AMR) AF: 0.0836 AC: 1279 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3466

East Asian (EAS) AF: 0.195 AC: 1012 AN: 5182

South Asian (SAS) AF: 0.108 AC: 521 AN: 4826

European-Finnish (FIN) AF: 0.0923 AC: 980 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0726 AC: 4940 AN: 68018

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0783 Hom.: 786

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
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs10493275; hg19: chr1-60455797;