NM_001080396.3:c.916-271806T>G

Variant names:

• chr13-107482561-A-C
• rs9520462
• NM_001080396.3:c.916-271806T>G

Variant summary

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

The NM_001080396.3(NALF1):​c.916-271806T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,230 control chromosomes in the GnomAD database, including 4,091 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 (4091 hom., cov: 33)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080396.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	NM_001080396.3	MANE Select	c.916-271806T>G		intron	N/A	NP_001073865.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	ENST00000375915.4	TSL:1 MANE Select	c.916-271806T>G		intron	N/A	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31162 AN: 152112 Hom.: 4092 Cov.: 33

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.205 AC: 31160 AN: 152230 Hom.: 4091 Cov.: 33 AF XY: 0.202 AC XY: 15008 AN XY: 74428

African (AFR) AF: 0.0522 AC: 2171 AN: 41566

American (AMR) AF: 0.224 AC: 3425 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3472

East Asian (EAS) AF: 0.142 AC: 738 AN: 5184

South Asian (SAS) AF: 0.168 AC: 811 AN: 4826

European-Finnish (FIN) AF: 0.257 AC: 2721 AN: 10598

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19514 AN: 67994

Other (OTH) AF: 0.223 AC: 472 AN: 2114

Alfa AF: 0.255 Hom.: 3396

Bravo AF: 0.198

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.49
PhyloP100		-0.089
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9520462; hg19: chr13-108134909;