13-107866358-TGCTGCTGCC-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001080396.3(NALF1):c.230_238del(p.Arg77_Gln79del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0122 in 1,610,692 control chromosomes in the GnomAD database, including 113 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0084 (7 hom., cov: 31)
  • Exomes 𝑓: 0.013 (106 hom.)
• Consequence: NALF1 NM_001080396.3 inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.83

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

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 13-107866358-TGCTGCTGCC-T is Benign according to our data. Variant chr13-107866358-TGCTGCTGCC-T is described in ClinVar as [Benign]. Clinvar id is 2643929.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NALF1	NM_001080396.3	c.230_238del	p.Arg77_Gln79del	inframe_deletion	1/3	ENST00000375915.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NALF1	ENST00000375915.4	c.230_238del	p.Arg77_Gln79del	inframe_deletion	1/3	1	NM_001080396.3	P1

Frequencies

GnomAD3 genomes AF: 0.00842 AC: 1278 AN: 151722 Hom.: 7 Cov.: 31

Gnomad AFR AF: 0.00275

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00288

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000997

Gnomad SAS AF: 0.000838

Gnomad FIN AF: 0.0130

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.00288

GnomAD3 exomes AF: 0.00821 AC: 1996 AN: 243126 Hom.: 7 AF XY: 0.00834 AC XY: 1108 AN XY: 132896

Gnomad AFR exome AF: 0.00292

Gnomad AMR exome AF: 0.00299

Gnomad ASJ exome AF: 0.00192

Gnomad EAS exome AF: 0.00146

Gnomad SAS exome AF: 0.00242

Gnomad FIN exome AF: 0.0140

Gnomad NFE exome AF: 0.0129

Gnomad OTH exome AF: 0.00670

GnomAD4 exome AF: 0.0126 AC: 18348 AN: 1458860 Hom.: 106 AF XY: 0.0124 AC XY: 8969 AN XY: 725786

Gnomad4 AFR exome AF: 0.00227

Gnomad4 AMR exome AF: 0.00316

Gnomad4 ASJ exome AF: 0.00272

Gnomad4 EAS exome AF: 0.000732

Gnomad4 SAS exome AF: 0.00208

Gnomad4 FIN exome AF: 0.0136

Gnomad4 NFE exome AF: 0.0149

Gnomad4 OTH exome AF: 0.00950

GnomAD4 genome AF: 0.00842 AC: 1278 AN: 151832 Hom.: 7 Cov.: 31 AF XY: 0.00815 AC XY: 605 AN XY: 74202

Gnomad4 AFR AF: 0.00274

Gnomad4 AMR AF: 0.00282

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00100

Gnomad4 SAS AF: 0.000839

Gnomad4 FIN AF: 0.0130

Gnomad4 NFE AF: 0.0142

Gnomad4 OTH AF: 0.00285

Alfa AF: 0.0137 Hom.: 1

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

NALF1: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs764534910; hg19: chr13-108518706;