rs9555369

Variant names:

• chr13-107559672-C-T
• rs9555369
• NM_001080396.3:c.915+306010G>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+306010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,852 control chromosomes in the GnomAD database, including 10,304 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 0.36 (10304 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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.915+306010G>A		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.915+306010G>A		intron	N/A	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54420 AN: 151734 Hom.: 10278 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.359 AC: 54493 AN: 151852 Hom.: 10304 Cov.: 32 AF XY: 0.368 AC XY: 27335 AN XY: 74190

African (AFR) AF: 0.391 AC: 16170 AN: 41382

American (AMR) AF: 0.447 AC: 6832 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 843 AN: 3462

East Asian (EAS) AF: 0.465 AC: 2380 AN: 5122

South Asian (SAS) AF: 0.395 AC: 1901 AN: 4816

European-Finnish (FIN) AF: 0.472 AC: 4968 AN: 10528

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20303 AN: 67944

Other (OTH) AF: 0.341 AC: 720 AN: 2112

Alfa AF: 0.315 Hom.: 34035

Bravo AF: 0.360

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.51
PhyloP100		-1.5
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: rs9555369; hg19: chr13-108212020;