rs1543002

Positions:

• chr13-107851008-C-T

Variant summary

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

The ENST00000375915.4(NALF1):​c.915+14674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,998 control chromosomes in the GnomAD database, including 26,985 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 0.58 (26985 hom., cov: 33)
• Consequence: NALF1 ENST00000375915.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

Genes affected

NALF1 (HGNC:33877): (NALCN channel auxiliary factor 1) Predicted to contribute to stretch-activated, cation-selective, calcium channel activity. Predicted to be involved in calcium ion import across plasma membrane. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.915+14674G>A		intron_variant		ENST00000375915.4	NP_001073865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4	c.915+14674G>A		intron_variant		1	NM_001080396.3	ENSP00000365080	P1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88172 AN: 151884 Hom.: 26965 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.581 AC: 88243 AN: 151998 Hom.: 26985 Cov.: 33 AF XY: 0.580 AC XY: 43062 AN XY: 74292

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.603

Alfa AF: 0.647 Hom.: 33845

Bravo AF: 0.564

Asia WGS AF: 0.444 AC: 1546 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1543002; hg19: chr13-108503356;