13-107420167-C-T

Position:

• chr13-107420167-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.916-209412G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,980 control chromosomes in the GnomAD database, including 3,616 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 0.21 (3616 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NALF1	NM_001080396.3	c.916-209412G>A		intron_variant		ENST00000375915.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALF1	ENST00000375915.4	c.916-209412G>A		intron_variant		1	NM_001080396.3	P1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31630 AN: 151862 Hom.: 3619 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.208 AC: 31629 AN: 151980 Hom.: 3616 Cov.: 32 AF XY: 0.205 AC XY: 15243 AN XY: 74278

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.228

Alfa AF: 0.192 Hom.: 777

Bravo AF: 0.208

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.54

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: rs1323672; hg19: chr13-108072515;