rs7997236

Variant names:

• chr13-107280744-G-A
• rs7997236
• NM_001080396.3:c.916-69989C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-107280744-G-A
• chr13-107280744-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080396.3(NALF1):​c.916-69989C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,064 control chromosomes in the GnomAD database, including 483 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 0.062 (483 hom., cov: 33)
• Consequence: NALF1 NM_001080396.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080396.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	NM_001080396.3	MANE Select	c.916-69989C>T		intron	N/A	NP_001073865.1	B1AL88

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALF1	ENST00000375915.4	TSL:1 MANE Select	c.916-69989C>T		intron	N/A	ENSP00000365080.1	B1AL88

Frequencies

GnomAD3 genomes AF: 0.0624 AC: 9486 AN: 151946 Hom.: 478 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0631

Gnomad SAS AF: 0.0620

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.0579

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

GnomAD4 genome AF: 0.0625 AC: 9500 AN: 152064 Hom.: 483 Cov.: 33 AF XY: 0.0613 AC XY: 4556 AN XY: 74334

African (AFR) AF: 0.116 AC: 4817 AN: 41470

American (AMR) AF: 0.106 AC: 1624 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3468

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5174

South Asian (SAS) AF: 0.0612 AC: 294 AN: 4806

European-Finnish (FIN) AF: 0.0112 AC: 118 AN: 10566

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0289 AC: 1966 AN: 68000

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0450 Hom.: 371

Bravo AF: 0.0755

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.49
DANN	Benign	0.58
PhyloP100		-0.84
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: rs7997236; hg19: chr13-107933092;