Genetic Variant NALCN-AS1:n.142-135293A>G (chr13-100877925-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000457843.1(NALCN-AS1):n.142-135293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 152,220 control chromosomes in the GnomAD database, including 1,352 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 0.079 ( 1352 hom., cov: 32)

Consequence

NALCN-AS1
ENST00000457843.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

0 publications found

Variant links:

Genes affected

NALCN-AS1 (HGNC:42743): (NALCN antisense RNA 1)

NALCN-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=-0.71).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALCN-AS1	NR_047687.1 link	n.142-135293A>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NALCN-AS1	ENST00000457843.1 link	n.142-135293A>G		intron_variant	Intron 2 of 7	2

Frequencies

GnomAD3 genomes

AF:

0.0790

AC:

12023

AN:

152100

Hom.:

1346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0359

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.0634

Gnomad SAS

AF:

0.0246

Gnomad FIN

AF:

0.0451

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00553

Gnomad OTH

AF:

0.0623

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

GnomAD4 genome

AF:

0.0792

AC:

12057

AN:

152220

Hom.:

1352

Cov.:

AF XY:

0.0792

AC XY:

5896

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.242

AC:

10046

AN:

41496

American (AMR)

AF:

0.0358

AC:

547

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00807

AC:

AN:

3470

East Asian (EAS)

AF:

0.0634

AC:

328

AN:

5174

South Asian (SAS)

AF:

0.0238

AC:

115

AN:

4824

European-Finnish (FIN)

AF:

0.0451

AC:

479

AN:

10624

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00551

AC:

375

AN:

68026

Other (OTH)

AF:

0.0640

AC:

135

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

465

929

1394

1858

2323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0537

Hom.:

110

Bravo

AF:

0.0854

Asia WGS

AF:

0.0570

AC:

198

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.67

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