13-107839244-C-T

Variant names:

• chr13-107839244-C-T
• rs1509091
• NM_001080396.3:c.915+26438G>A

Variant summary

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

The NM_001080396.3(NALF1):​c.915+26438G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 150,952 control chromosomes in the GnomAD database, including 56,889 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 0.86 (56889 hom., cov: 25)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.912 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	NM_001080396.3	MANE Select	c.915+26438G>A		intron	N/A	NP_001073865.1	B1AL88

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	ENST00000375915.4	TSL:1 MANE Select	c.915+26438G>A		intron	N/A	ENSP00000365080.1	B1AL88

Frequencies

GnomAD3 genomes AF: 0.863 AC: 130245 AN: 150834 Hom.: 56858 Cov.: 25

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.863 AC: 130331 AN: 150952 Hom.: 56889 Cov.: 25 AF XY: 0.864 AC XY: 63678 AN XY: 73670

African (AFR) AF: 0.725 AC: 29656 AN: 40930

American (AMR) AF: 0.925 AC: 13976 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3135 AN: 3468

East Asian (EAS) AF: 0.909 AC: 4644 AN: 5108

South Asian (SAS) AF: 0.848 AC: 4020 AN: 4738

European-Finnish (FIN) AF: 0.928 AC: 9707 AN: 10462

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62314 AN: 67844

Other (OTH) AF: 0.873 AC: 1820 AN: 2084

Alfa AF: 0.894 Hom.: 112973

Bravo AF: 0.860

Asia WGS AF: 0.845 AC: 2939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.51
PhyloP100		-0.24
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: rs1509091; hg19: chr13-108491592;