13-107485140-T-C

Variant names:

• chr13-107485140-T-C
• rs1408015
• NM_001080396.3:c.916-274385A>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.916-274385A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,944 control chromosomes in the GnomAD database, including 36,771 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 0.69 (36771 hom., cov: 31)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 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.916-274385A>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.916-274385A>G		intron	N/A	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104436 AN: 151826 Hom.: 36774 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.687 AC: 104461 AN: 151944 Hom.: 36771 Cov.: 31 AF XY: 0.685 AC XY: 50868 AN XY: 74252

African (AFR) AF: 0.559 AC: 23154 AN: 41412

American (AMR) AF: 0.620 AC: 9464 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2635 AN: 3468

East Asian (EAS) AF: 0.590 AC: 3028 AN: 5130

South Asian (SAS) AF: 0.688 AC: 3307 AN: 4806

European-Finnish (FIN) AF: 0.781 AC: 8261 AN: 10572

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52128 AN: 67978

Other (OTH) AF: 0.710 AC: 1500 AN: 2112

Alfa AF: 0.695 Hom.: 6856

Bravo AF: 0.669

Asia WGS AF: 0.616 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.52
DANN	Benign	0.29
PhyloP100		-0.056
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: rs1408015; hg19: chr13-108137488;