chr13-107675800-T-C

Variant names:

• chr13-107675800-T-C
• rs7328649
• NM_001080396.3:c.915+189882A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080396.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	NM_001080396.3	MANE Select	c.915+189882A>G		intron	N/A	NP_001073865.1	B1AL88

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	ENST00000375915.4	TSL:1 MANE Select	c.915+189882A>G		intron	N/A	ENSP00000365080.1	B1AL88

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

African (AFR) AF: 0.0820 AC: 3404 AN: 41532

American (AMR) AF: 0.0687 AC: 1050 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1296 AN: 5170

South Asian (SAS) AF: 0.0964 AC: 465 AN: 4826

European-Finnish (FIN) AF: 0.0172 AC: 183 AN: 10616

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0104 AC: 706 AN: 68018

Other (OTH) AF: 0.0473 AC: 100 AN: 2114

Alfa AF: 0.0297 Hom.: 326

Bravo AF: 0.0544

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.62
PhyloP100		-3.1
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: rs7328649; hg19: chr13-108328148;