NM_001080396.3:c.916-233023C>A

Variant names:

• chr13-107443778-G-T
• rs1924174
• NM_001080396.3:c.916-233023C>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.916-233023C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,896 control chromosomes in the GnomAD database, including 4,849 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 0.24 (4849 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.916-233023C>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.916-233023C>A		intron_variant	Intron 1 of 2	1	NM_001080396.3	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36375 AN: 151778 Hom.: 4847 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.239 AC: 36367 AN: 151896 Hom.: 4849 Cov.: 32 AF XY: 0.241 AC XY: 17863 AN XY: 74236

African (AFR) AF: 0.123 AC: 5111 AN: 41444

American (AMR) AF: 0.209 AC: 3192 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3464

East Asian (EAS) AF: 0.334 AC: 1721 AN: 5154

South Asian (SAS) AF: 0.258 AC: 1237 AN: 4802

European-Finnish (FIN) AF: 0.333 AC: 3505 AN: 10514

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19585 AN: 67936

Other (OTH) AF: 0.257 AC: 542 AN: 2112

Alfa AF: 0.261 Hom.: 1443

Bravo AF: 0.222

Asia WGS AF: 0.267 AC: 926 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.015
DANN	Benign	0.32
PhyloP100		-2.6
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: rs1924174; hg19: chr13-108096126;