ENST00000479039.3:n.145-3900A>G

Variant names:

• chr3-109132944-A-G
• rs4441659
• ENST00000479039.3:n.145-3900A>G

Variant summary

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

The ENST00000479039.3(C3orf85):​n.145-3900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,078 control chromosomes in the GnomAD database, including 49,185 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 0.80 (49185 hom., cov: 31)
• Consequence: C3orf85 ENST00000479039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

C3orf85 (HGNC:53432): (chromosome 3 open reading frame 85)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 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
C3orf85	ENST00000479039.3	n.145-3900A>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121270 AN: 151960 Hom.: 49148 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.798 AC: 121356 AN: 152078 Hom.: 49185 Cov.: 31 AF XY: 0.802 AC XY: 59665 AN XY: 74360

Gnomad4 AFR AF: 0.649 AC: 0.648972 AN: 0.648972

Gnomad4 AMR AF: 0.863 AC: 0.863107 AN: 0.863107

Gnomad4 ASJ AF: 0.794 AC: 0.794236 AN: 0.794236

Gnomad4 EAS AF: 0.926 AC: 0.925754 AN: 0.925754

Gnomad4 SAS AF: 0.847 AC: 0.84732 AN: 0.84732

Gnomad4 FIN AF: 0.889 AC: 0.888532 AN: 0.888532

Gnomad4 NFE AF: 0.846 AC: 0.846163 AN: 0.846163

Gnomad4 OTH AF: 0.795 AC: 0.794981 AN: 0.794981

Alfa AF: 0.832 Hom.: 213988

Bravo AF: 0.790

Asia WGS AF: 0.857 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.29
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4441659; hg19: chr3-108851791;