13-107675605-C-T

Variant names:

• chr13-107675605-C-T
• rs1935132
• NM_001080396.3:c.915+190077G>A

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+190077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,912 control chromosomes in the GnomAD database, including 14,644 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 0.42 (14644 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.915+190077G>A		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.915+190077G>A		intron_variant	Intron 1 of 2	1	NM_001080396.3	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64099 AN: 151794 Hom.: 14645 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.422 AC: 64129 AN: 151912 Hom.: 14644 Cov.: 32 AF XY: 0.431 AC XY: 31988 AN XY: 74246

African (AFR) AF: 0.239 AC: 9912 AN: 41436

American (AMR) AF: 0.512 AC: 7826 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1570 AN: 3468

East Asian (EAS) AF: 0.577 AC: 2959 AN: 5124

South Asian (SAS) AF: 0.447 AC: 2153 AN: 4812

European-Finnish (FIN) AF: 0.610 AC: 6419 AN: 10522

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31952 AN: 67968

Other (OTH) AF: 0.406 AC: 852 AN: 2100

Alfa AF: 0.454 Hom.: 25682

Bravo AF: 0.407

Asia WGS AF: 0.514 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.42
PhyloP100		-1.9
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: rs1935132; hg19: chr13-108327953;