13-107832106-G-A

Position:

• chr13-107832106-G-A

Variant summary

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

The NM_001080396.3(NALF1):​c.915+33576C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,984 control chromosomes in the GnomAD database, including 2,953 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 0.16 (2953 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

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]

NALF1-IT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.915+33576C>T		intron_variant		ENST00000375915.4	NP_001073865.1
NALF1-IT1	NR_046848.1	n.57+3296C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4	c.915+33576C>T		intron_variant		1	NM_001080396.3	ENSP00000365080.1
NALF1-IT1	ENST00000449551.1	n.50+3296C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24801 AN: 151866 Hom.: 2951 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.163 AC: 24828 AN: 151984 Hom.: 2953 Cov.: 32 AF XY: 0.163 AC XY: 12114 AN XY: 74302

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0880

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.153

Alfa AF: 0.0927 Hom.: 1364

Bravo AF: 0.179

Asia WGS AF: 0.179 AC: 617 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.24

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: rs2036707; hg19: chr13-108484454;