13-107219364-G-C

Variant names:

• chr13-107219364-G-C
• rs16969868
• NM_001080396.3:c.916-8609C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375915.4(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 ENST00000375915.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375915.4. 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.916-8609C>G		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.916-8609C>G		intron	N/A	ENSP00000365080.1

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

African (AFR) AF: 0.0609 AC: 2528 AN: 41514

American (AMR) AF: 0.0361 AC: 552 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3470

East Asian (EAS) AF: 0.0834 AC: 432 AN: 5178

South Asian (SAS) AF: 0.0778 AC: 375 AN: 4822

European-Finnish (FIN) AF: 0.00387 AC: 41 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0217 AC: 1475 AN: 68028

Other (OTH) AF: 0.0417 AC: 88 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		0.24
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: rs16969868; hg19: chr13-107871712;