Genetic Variant ENST00000479039.3:n.145-3900A>G (chr3-109132944-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The ENST00000479039.3(C3orf85):n.145-3900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000479039.3 is not a MANE Select or MANE Plus Clinical transcript for C3orf85; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.798 (AC=121,356) in the gnomAD database across 152,078 control chromosomes, including 49,185 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.904. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.09

Publications

7 publications found

Variant links:

Genes affected

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

C3orf85 links:

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new If you want to explore the variant's impact on the transcript ENST00000479039.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

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

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.9039 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000479039.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3orf85	ENST00000479039.3	TSL:5	n.145-3900A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.798

AC:

121270

AN:

151960

Hom.:

49148

Cov.:

show subpopulations

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.:

AF XY:

0.802

AC XY:

59665

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.649

AC:

26896

AN:

41444

American (AMR)

AF:

0.863

AC:

13190

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.794

AC:

2756

AN:

3470

East Asian (EAS)

AF:

0.926

AC:

4788

AN:

5172

South Asian (SAS)

AF:

0.847

AC:

4079

AN:

4814

European-Finnish (FIN)

AF:

0.889

AC:

9406

AN:

10586

Middle Eastern (MID)

AF:

0.772

AC:

227

AN:

294

European-Non Finnish (NFE)

AF:

0.846

AC:

57534

AN:

67994

Other (OTH)

AF:

0.795

AC:

1679

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1184

2368

3553

4737

5921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

864

1728

2592

3456

4320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.832

Hom.:

213988

Bravo

AF:

0.790

Asia WGS

AF:

0.857

AC:

2981

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.970

AC:

119164

AN:

122802

Turkish Variome

AF:

0.847

AC:

1309

AN:

1546

Hom.:

560

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.923

AC:

8267

AN:

8960

Hom.:

3818

ABraOM SABE-WGS-1171

AF:

0.813

AC:

1904

AN:

2342

Hom.:

770

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.29

(source)

DANN

Benign

0.33

PhyloP100

-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over