rs6625472

chrX-69519699-C-T

Variant summary

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

The NM_015686.3(NALF2):c.862-9294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 111,735 control chromosomes in the GnomAD database, including 1,739 homozygotes. There are 5,926 hemizygotes in GnomAD. 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 0.18 (1739 hom., 5926 hem., cov: 23)
• Consequence: NALF2 NM_015686.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

Genes affected

NALF2 (HGNC:30701): (NALCN channel auxiliary factor 2) This gene encodes a product belonging to a family of proteins with unknown function. The presence of two transmembrane domains suggests that this protein is a multi-pass membrane protein. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NALF2	NM_015686.3	c.862-9294C>T		intron_variant		ENST00000252338.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALF2	ENST00000252338.5	c.862-9294C>T		intron_variant		1	NM_015686.3	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 20015 AN: 111680 Hom.: 1740 Cov.: 23 AF XY: 0.175 AC XY: 5924 AN XY: 33872

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.179 AC: 20010 AN: 111735 Hom.: 1739 Cov.: 23 AF XY: 0.175 AC XY: 5926 AN XY: 33937

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0390

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.165

Alfa AF: 0.244 Hom.: 5864

Bravo AF: 0.157

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	5.2
Dann	Benign	0.92

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: rs6625472; hg19: chrX-68739542;