rs927821

Variant names:

• chr10-102448042-C-A
• rs927821
• ENST00000755282.1:n.42-1637C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-102448042-C-A
• chr10-102448042-C-G
• chr10-102448042-C-T

Variant summary

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

The ENST00000755282.1(C10orf95-AS1):​n.42-1637C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,058 control chromosomes in the GnomAD database, including 54,990 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 0.85 (54990 hom., cov: 30)
• Consequence: C10orf95-AS1 ENST00000755282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862
• Publications: 7 publications found

Genes affected

C10orf95-AS1 (HGNC:45238): (C10orf95 antisense RNA 1)

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 (SAS) allele frequency at 95% confidence interval = 0.905 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
C10orf95-AS1	ENST00000755282.1	n.42-1637C>A		intron_variant	Intron 1 of 3
C10orf95-AS1	ENST00000755283.1	n.42-1637C>A		intron_variant	Intron 1 of 3
C10orf95-AS1	ENST00000755284.1	n.240-1637C>A		intron_variant	Intron 1 of 3
C10orf95-AS1	ENST00000755285.1	n.42-1637C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129015 AN: 151940 Hom.: 54939 Cov.: 30

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.849 AC: 129125 AN: 152058 Hom.: 54990 Cov.: 30 AF XY: 0.850 AC XY: 63185 AN XY: 74296

African (AFR) AF: 0.912 AC: 37859 AN: 41498

American (AMR) AF: 0.861 AC: 13124 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3470

East Asian (EAS) AF: 0.813 AC: 4192 AN: 5158

South Asian (SAS) AF: 0.915 AC: 4416 AN: 4824

European-Finnish (FIN) AF: 0.805 AC: 8493 AN: 10552

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55560 AN: 67996

Other (OTH) AF: 0.829 AC: 1750 AN: 2110

Alfa AF: 0.830 Hom.: 143633

Bravo AF: 0.856

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.87
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs927821; hg19: chr10-104207799;