rs753708

Variant names:

• chr13-100769115-A-C
• rs753708
• ENST00000457843.1:n.141+28487A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-100769115-A-C
• chr13-100769115-A-T

Variant summary

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

The ENST00000457843.1(NALCN-AS1):​n.141+28487A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,230 control chromosomes in the GnomAD database, including 819 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 0.099 (819 hom., cov: 33)
• Consequence: NALCN-AS1 ENST00000457843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALCN-AS1	NR_047687.1	n.141+28487A>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NALCN-AS1	ENST00000457843.1	n.141+28487A>C		intron_variant	Intron 2 of 7	2

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 15121 AN: 152112 Hom.: 819 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0994 AC: 15126 AN: 152230 Hom.: 819 Cov.: 33 AF XY: 0.103 AC XY: 7652 AN XY: 74438

African (AFR) AF: 0.117 AC: 4844 AN: 41534

American (AMR) AF: 0.101 AC: 1544 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3470

East Asian (EAS) AF: 0.159 AC: 820 AN: 5172

South Asian (SAS) AF: 0.153 AC: 740 AN: 4824

European-Finnish (FIN) AF: 0.116 AC: 1231 AN: 10600

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.0790 AC: 5372 AN: 68020

Other (OTH) AF: 0.105 AC: 221 AN: 2114

Alfa AF: 0.0824 Hom.: 943

Bravo AF: 0.0979

Asia WGS AF: 0.169 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs753708; hg19: chr13-101421369;