13-107575531-A-G

Variant names:

• chr13-107575531-A-G
• rs9301233
• NM_001080396.3:c.915+290151T>C

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+290151T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,978 control chromosomes in the GnomAD database, including 11,346 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 0.37 (11346 hom., cov: 31)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.915+290151T>C		intron_variant	Intron 1 of 2	ENST00000375915.4	NP_001073865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4	c.915+290151T>C		intron_variant	Intron 1 of 2	1	NM_001080396.3	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56133 AN: 151860 Hom.: 11343 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.370 AC: 56169 AN: 151978 Hom.: 11346 Cov.: 31 AF XY: 0.368 AC XY: 27373 AN XY: 74292

African (AFR) AF: 0.210 AC: 8704 AN: 41486

American (AMR) AF: 0.386 AC: 5899 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1943 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1522 AN: 5136

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4025 AN: 10542

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 30045 AN: 67926

Other (OTH) AF: 0.421 AC: 891 AN: 2114

Alfa AF: 0.436 Hom.: 7733

Bravo AF: 0.362

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		-0.11
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: rs9301233; hg19: chr13-108227879;