Genetic Variant CALML3-AS1:n.112-14080C>T (chr10-5536209-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000770238.1(CALML3-AS1):n.112-14080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,086 control chromosomes in the GnomAD database, including 1,892 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 0.14 ( 1892 hom., cov: 31)

Consequence

CALML3-AS1
ENST00000770238.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Publications

4 publications found

Variant links:

Genes affected

CALML3-AS1 (HGNC:44682): (CALML3 antisense RNA 1)

CALML3-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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CALML3-AS1	ENST00000770238.1 link	n.112-14080C>T	intron_variant	Intron 1 of 2
CALML3-AS1	ENST00000770239.1 link	n.203+11978C>T	intron_variant	Intron 1 of 2
CALML3-AS1	ENST00000770240.1 link	n.154+11978C>T	intron_variant	Intron 1 of 1
CALML3-AS1	ENST00000770241.1 link	n.127-5071C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21115

AN:

151968

Hom.:

1895

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0371

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.216

Gnomad ASJ

AF:

0.0617

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.135

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

GnomAD4 genome

AF:

0.139

AC:

21115

AN:

152086

Hom.:

1892

Cov.:

AF XY:

0.140

AC XY:

10382

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.0370

AC:

1535

AN:

41490

American (AMR)

AF:

0.216

AC:

3299

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0617

AC:

214

AN:

3468

East Asian (EAS)

AF:

0.142

AC:

736

AN:

5172

South Asian (SAS)

AF:

0.166

AC:

797

AN:

4810

European-Finnish (FIN)

AF:

0.162

AC:

1713

AN:

10562

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.181

AC:

12322

AN:

67982

Other (OTH)

AF:

0.134

AC:

284

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

913

1827

2740

3654

4567

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.163

Hom.:

3925

Bravo

AF:

0.140

Asia WGS

AF:

0.148

AC:

514

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.5

(source)

DANN

Benign

0.25

PhyloP100

1.0

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