13-107298929-A-G

Variant names:

• chr13-107298929-A-G
• rs7999230
• NM_001080396.3:c.916-88174T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080396.3(NALF1):​c.916-88174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,762 control chromosomes in the GnomAD database, including 5,751 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 0.27 (5751 hom., cov: 31)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.916-88174T>C		intron_variant	Intron 1 of 2	ENST00000375915.4	NP_001073865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4	c.916-88174T>C		intron_variant	Intron 1 of 2	1	NM_001080396.3	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40415 AN: 151644 Hom.: 5744 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.266 AC: 40436 AN: 151762 Hom.: 5751 Cov.: 31 AF XY: 0.263 AC XY: 19477 AN XY: 74158

African (AFR) AF: 0.276 AC: 11399 AN: 41244

American (AMR) AF: 0.180 AC: 2748 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3466

East Asian (EAS) AF: 0.0385 AC: 199 AN: 5164

South Asian (SAS) AF: 0.137 AC: 661 AN: 4820

European-Finnish (FIN) AF: 0.342 AC: 3597 AN: 10528

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20194 AN: 67960

Other (OTH) AF: 0.236 AC: 498 AN: 2108

Alfa AF: 0.282 Hom.: 3015

Bravo AF: 0.253

Asia WGS AF: 0.106 AC: 371 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	2.2
DANN	Benign	0.70
PhyloP100		0.59
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: rs7999230; hg19: chr13-107951277;