chr13-107810871-T-C

Variant names:

• chr13-107810871-T-C
• rs3905075
• NM_001080396.3:c.915+54811A>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+54811A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,992 control chromosomes in the GnomAD database, including 32,465 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 0.65 (32465 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 7 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]

NALF1-IT1 (HGNC:41503): (NALF1 intronic transcript 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 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+54811A>G		intron	N/A	NP_001073865.1	B1AL88
	NALF1-IT1	NR_046848.1		n.58-21761A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	ENST00000375915.4	TSL:1 MANE Select	c.915+54811A>G		intron	N/A	ENSP00000365080.1	B1AL88
	NALF1-IT1	ENST00000449551.1	TSL:1	n.51-21761A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98308 AN: 151874 Hom.: 32422 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.647 AC: 98407 AN: 151992 Hom.: 32465 Cov.: 32 AF XY: 0.644 AC XY: 47823 AN XY: 74316

African (AFR) AF: 0.759 AC: 31456 AN: 41458

American (AMR) AF: 0.675 AC: 10300 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3700 AN: 5162

South Asian (SAS) AF: 0.582 AC: 2813 AN: 4830

European-Finnish (FIN) AF: 0.565 AC: 5960 AN: 10556

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.588 AC: 39967 AN: 67946

Other (OTH) AF: 0.643 AC: 1357 AN: 2112

Alfa AF: 0.609 Hom.: 76305

Bravo AF: 0.666

Asia WGS AF: 0.628 AC: 2185 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.26
PhyloP100		0.011
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: rs3905075; hg19: chr13-108463219;