rs9555369

chr13-107559672-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NALF1	NM_001080396.3	c.915+306010G>A		intron_variant		ENST00000375915.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALF1	ENST00000375915.4	c.915+306010G>A		intron_variant		1	NM_001080396.3	P1

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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.341

Alfa AF: 0.308 Hom.: 16009

Bravo AF: 0.360

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.16
Dann	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs9555369; hg19: chr13-108212020;