rs744134

chr13-107471973-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080396.3(NALF1):c.916-261218A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,158 control chromosomes in the GnomAD database, including 6,598 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 0.27 (6598 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NALF1	NM_001080396.3	c.916-261218A>G		intron_variant		ENST00000375915.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALF1	ENST00000375915.4	c.916-261218A>G		intron_variant		1	NM_001080396.3	P1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41171 AN: 152040 Hom.: 6595 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.271 AC: 41187 AN: 152158 Hom.: 6598 Cov.: 32 AF XY: 0.270 AC XY: 20101 AN XY: 74372

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.299

Alfa AF: 0.337 Hom.: 4205

Bravo AF: 0.259

Asia WGS AF: 0.273 AC: 948 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	1.5
Dann	Benign	0.64

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: rs744134; hg19: chr13-108124321;