Genetic Variant CLCA4-AS1:n.295-14110G>A (chr1-86585518-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000456587.1(CLCA4-AS1):n.295-14110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,828 control chromosomes in the GnomAD database, including 7,526 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 0.31 ( 7526 hom., cov: 32)

Consequence

CLCA4-AS1
ENST00000456587.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.281

Publications

7 publications found

Variant links:

Genes affected

CLCA4-AS1 (HGNC:54055): (CLCA4 antisense RNA 1)

CLCA4-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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLCA4-AS1	NR_135837.1 link	n.1293-14110G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CLCA4-AS1	ENST00000456587.1 link	n.295-14110G>A	intron_variant	Intron 3 of 3	3
CLCA4-AS1	ENST00000650379.2 link	n.2183-475G>A	intron_variant	Intron 3 of 4
CLCA4-AS1	ENST00000699483.1 link	n.1284-14110G>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47638

AN:

151710

Hom.:

7521

Cov.:

show subpopulations

Gnomad AFR

AF:

0.290

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.270

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.273

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.339

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

GnomAD4 genome

AF:

0.314

AC:

47658

AN:

151828

Hom.:

7526

Cov.:

AF XY:

0.310

AC XY:

23028

AN XY:

74174

show subpopulations

African (AFR)

AF:

0.290

AC:

12000

AN:

41406

American (AMR)

AF:

0.270

AC:

4119

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1232

AN:

3468

East Asian (EAS)

AF:

0.273

AC:

1401

AN:

5132

South Asian (SAS)

AF:

0.214

AC:

1034

AN:

4822

European-Finnish (FIN)

AF:

0.337

AC:

3549

AN:

10526

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23314

AN:

67916

Other (OTH)

AF:

0.338

AC:

712

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1648

3297

4945

6594

8242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.333

Hom.:

22512

Bravo

AF:

0.310

Asia WGS

AF:

0.245

AC:

850

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

0.98

(source)

DANN

Benign

0.51

PhyloP100

-0.28

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