13-107629573-G-A

Variant names:

• chr13-107629573-G-A
• rs719185
• NM_001080396.3:c.915+236109C>T

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+236109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,840 control chromosomes in the GnomAD database, including 27,924 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 0.58 (27924 hom., cov: 31)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.915+236109C>T		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+236109C>T		intron_variant	Intron 1 of 2	1	NM_001080396.3	ENSP00000365080.1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87878 AN: 151722 Hom.: 27914 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.579 AC: 87921 AN: 151840 Hom.: 27924 Cov.: 31 AF XY: 0.586 AC XY: 43479 AN XY: 74216

African (AFR) AF: 0.319 AC: 13204 AN: 41362

American (AMR) AF: 0.727 AC: 11082 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1967 AN: 3468

East Asian (EAS) AF: 0.995 AC: 5135 AN: 5160

South Asian (SAS) AF: 0.600 AC: 2887 AN: 4812

European-Finnish (FIN) AF: 0.697 AC: 7357 AN: 10552

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44209 AN: 67934

Other (OTH) AF: 0.632 AC: 1332 AN: 2108

Alfa AF: 0.622 Hom.: 14271

Bravo AF: 0.573

Asia WGS AF: 0.761 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.067
DANN	Benign	0.66
PhyloP100		-0.81
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: rs719185; hg19: chr13-108281921;