rs10508046

chr13-100877925-A-G

Variant summary

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

The NR_047687.1(NALCN-AS1):n.142-135293A>G 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 0.0792 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 NR_047687.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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=-0.71).
• 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/exons	MANE	UniProt
NALCN-AS1	NR_047687.1	n.142-135293A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALCN-AS1	ENST00000457843.1	n.142-135293A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.0358

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.0634

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.00551

Gnomad4 OTH AF: 0.0640

Alfa AF: 0.0468 Hom.: 87

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	11
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508046; hg19: chr13-101530179;