chr13-107604872-T-C

Variant names:

• chr13-107604872-T-C
• rs957788
• NM_001080396.3:c.915+260810A>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+260810A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,896 control chromosomes in the GnomAD database, including 9,702 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 0.35 (9702 hom., cov: 32)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.915+260810A>G		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+260810A>G		intron_variant	Intron 1 of 2	1	NM_001080396.3	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52677 AN: 151778 Hom.: 9699 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0842

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.347 AC: 52719 AN: 151896 Hom.: 9702 Cov.: 32 AF XY: 0.341 AC XY: 25341 AN XY: 74250

African (AFR) AF: 0.458 AC: 18934 AN: 41366

American (AMR) AF: 0.304 AC: 4639 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1214 AN: 3462

East Asian (EAS) AF: 0.0842 AC: 435 AN: 5168

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4822

European-Finnish (FIN) AF: 0.251 AC: 2656 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22064 AN: 67936

Other (OTH) AF: 0.322 AC: 681 AN: 2112

Alfa AF: 0.333 Hom.: 29573

Bravo AF: 0.354

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.51
PhyloP100		-1.2
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: rs957788; hg19: chr13-108257220;