13-100999406-G-A

Position:

• chr13-100999406-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047687.1(NALCN-AS1):​n.142-13812G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,118 control chromosomes in the GnomAD database, including 3,422 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 0.20 (3422 hom., cov: 32)
• Consequence: NALCN-AS1 NR_047687.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NALCN-AS1	NR_047687.1	n.142-13812G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALCN-AS1	ENST00000457843.1	n.142-13812G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29783 AN: 151998 Hom.: 3423 Cov.: 32

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.196 AC: 29780 AN: 152118 Hom.: 3422 Cov.: 32 AF XY: 0.193 AC XY: 14365 AN XY: 74368

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.196

Alfa AF: 0.231 Hom.: 553

Bravo AF: 0.188

Asia WGS AF: 0.161 AC: 558 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	0.88
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536231; hg19: chr13-101651758;