rs2765315

Variant names:

• chr13-101019693-A-G
• rs2765315
• ENST00000457843.1:n.275-4986A>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.275-4986A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,098 control chromosomes in the GnomAD database, including 55,811 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 0.86 (55811 hom., cov: 30)
• Consequence: NALCN-AS1 ENST00000457843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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.275-4986A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALCN-AS1	ENST00000457843.1	TSL:2	n.275-4986A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130066 AN: 151980 Hom.: 55772 Cov.: 30

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.856 AC: 130163 AN: 152098 Hom.: 55811 Cov.: 30 AF XY: 0.857 AC XY: 63690 AN XY: 74348

African (AFR) AF: 0.829 AC: 34360 AN: 41464

American (AMR) AF: 0.899 AC: 13761 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3182 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4747 AN: 5158

South Asian (SAS) AF: 0.846 AC: 4070 AN: 4810

European-Finnish (FIN) AF: 0.872 AC: 9233 AN: 10588

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57891 AN: 67986

Other (OTH) AF: 0.861 AC: 1820 AN: 2114

Alfa AF: 0.861 Hom.: 84438

Bravo AF: 0.861

Asia WGS AF: 0.878 AC: 3054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.69
DANN	Benign	0.37
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2765315; hg19: chr13-101672045;