13-107823165-C-T

Position:

• chr13-107823165-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375915.4(NALF1):​c.915+42517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,062 control chromosomes in the GnomAD database, including 12,781 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 0.38 (12781 hom., cov: 33)
• Consequence: NALF1 ENST00000375915.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NALF1	NM_001080396.3	c.915+42517G>A		intron_variant		ENST00000375915.4	NP_001073865.1
NALF1-IT1	NR_046848.1	n.57+12237G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4	c.915+42517G>A		intron_variant		1	NM_001080396.3	ENSP00000365080	P1
NALF1-IT1	ENST00000449551.1	n.50+12237G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57767 AN: 151944 Hom.: 12738 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.381 AC: 57867 AN: 152062 Hom.: 12781 Cov.: 33 AF XY: 0.387 AC XY: 28783 AN XY: 74342

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.352

Alfa AF: 0.314 Hom.: 4040

Bravo AF: 0.393

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs7325927; hg19: chr13-108475513;