rs7328649

Positions:

• chr13-107675800-T-C

Variant summary

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

The NM_001080396.3(NALF1):​c.915+189882A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 152,248 control chromosomes in the GnomAD database, including 401 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 0.048 (401 hom., cov: 33)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NALF1	NM_001080396.3	c.915+189882A>G		intron_variant		ENST00000375915.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALF1	ENST00000375915.4	c.915+189882A>G		intron_variant		1	NM_001080396.3	P1

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7292 AN: 152130 Hom.: 390 Cov.: 33

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.0172

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0483 AC: 7352 AN: 152248 Hom.: 401 Cov.: 33 AF XY: 0.0511 AC XY: 3808 AN XY: 74458

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.0687

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0964

Gnomad4 FIN AF: 0.0172

Gnomad4 NFE AF: 0.0104

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0373 Hom.: 39

Bravo AF: 0.0544

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.62

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: rs7328649; hg19: chr13-108328148;