13-107219364-G-C

Position:

• chr13-107219364-G-C

Variant summary

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

The NM_001080396.3(NALF1):​c.916-8609C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0388 in 152,224 control chromosomes in the GnomAD database, including 161 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 0.039 (161 hom., cov: 33)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.916-8609C>G		intron_variant		ENST00000375915.4	NP_001073865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4	c.916-8609C>G		intron_variant		1	NM_001080396.3	ENSP00000365080	P1

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5892 AN: 152104 Hom.: 157 Cov.: 33

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.0831

Gnomad SAS AF: 0.0789

Gnomad FIN AF: 0.00387

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0388 AC: 5903 AN: 152224 Hom.: 161 Cov.: 33 AF XY: 0.0396 AC XY: 2944 AN XY: 74430

Gnomad4 AFR AF: 0.0609

Gnomad4 AMR AF: 0.0361

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.0834

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.00387

Gnomad4 NFE AF: 0.0217

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.00993 Hom.: 2

Bravo AF: 0.0421

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.67

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: rs16969868; hg19: chr13-107871712;