13-107195084-C-T

Variant names:

• chr13-107195084-C-T
• rs9301196
• NM_001080396.3:c.1087+15500G>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.1087+15500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,018 control chromosomes in the GnomAD database, including 8,594 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 0.31 (8594 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.1087+15500G>A		intron_variant	Intron 2 of 2	ENST00000375915.4	NP_001073865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4	c.1087+15500G>A		intron_variant	Intron 2 of 2	1	NM_001080396.3	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46424 AN: 151900 Hom.: 8593 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.305 AC: 46419 AN: 152018 Hom.: 8594 Cov.: 32 AF XY: 0.304 AC XY: 22601 AN XY: 74308

African (AFR) AF: 0.0998 AC: 4139 AN: 41492

American (AMR) AF: 0.309 AC: 4720 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1676 AN: 3466

East Asian (EAS) AF: 0.215 AC: 1110 AN: 5174

South Asian (SAS) AF: 0.384 AC: 1844 AN: 4808

European-Finnish (FIN) AF: 0.378 AC: 3991 AN: 10548

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27539 AN: 67936

Other (OTH) AF: 0.355 AC: 747 AN: 2106

Alfa AF: 0.338 Hom.: 1638

Bravo AF: 0.288

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.63
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: rs9301196; hg19: chr13-107847432;