Genetic Variant CCL3-AS1:n.544-1978T>C (chr17-36087568-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000615750.2(CCL3-AS1):n.544-1978T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,086 control chromosomes in the GnomAD database, including 3,659 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 0.21 ( 3659 hom., cov: 31)

Consequence

CCL3-AS1
ENST00000615750.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.404

Publications

4 publications found

Variant links:

Genes affected

CCL3-AS1 (HGNC:55229): (CCL3 antisense RNA 1)

CCL3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL3-AS1	NR_186417.1 link	n.330-1978T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCL3-AS1	ENST00000615750.2 link	n.544-1978T>C	intron_variant	Intron 3 of 3	3
CCL3-AS1	ENST00000620056.4 link	n.390-1978T>C	intron_variant	Intron 3 of 3	5
CCL3-AS1	ENST00000818634.1 link	n.335-1978T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32480

AN:

151968

Hom.:

3654

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.345

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.214

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

GnomAD4 genome

AF:

0.214

AC:

32488

AN:

152086

Hom.:

3659

Cov.:

AF XY:

0.211

AC XY:

15675

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.174

AC:

7232

AN:

41488

American (AMR)

AF:

0.202

AC:

3081

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

613

AN:

3460

East Asian (EAS)

AF:

0.345

AC:

1778

AN:

5158

South Asian (SAS)

AF:

0.237

AC:

1144

AN:

4820

European-Finnish (FIN)

AF:

0.156

AC:

1654

AN:

10594

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.238

AC:

16196

AN:

67972

Other (OTH)

AF:

0.212

AC:

447

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1246

2492

3738

4984

6230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.230

Hom.:

10034

Bravo

AF:

0.218

Asia WGS

AF:

0.311

AC:

1081

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

(source)

DANN

Benign

0.78

PhyloP100

-0.40

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over