rs10508046

Variant names:

• chr13-100877925-A-G
• rs10508046
• ENST00000457843.1:n.142-135293A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 0 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457843.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALCN-AS1	NR_047687.1		n.142-135293A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALCN-AS1	ENST00000457843.1	TSL:2	n.142-135293A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 12023 AN: 152100 Hom.: 1346 Cov.: 32

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.: 32 AF XY: 0.0792 AC XY: 5896 AN XY: 74440

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: 28 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: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00551 AC: 375 AN: 68026

Other (OTH) AF: 0.0640 AC: 135 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		1.0

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.

Other links and lift over

dbSNP: rs10508046;

hg19: chr13-101530179;