Variant 13-107170569-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001080396.3(NALF1):c.1305A>G(p.Ala435Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0038 in 1,614,176 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0038 ( 28 hom. )

Consequence

NALF1
NM_001080396.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.610

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 13-107170569-T-C is Benign according to our data. Variant chr13-107170569-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2643928.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.61 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NALF1	NM_001080396.3 linkuse as main transcript	c.1305A>G	p.Ala435Ala	synonymous_variant	3/3	ENST00000375915.4	NP_001073865.1	B1AL88

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NALF1	ENST00000375915.4 linkuse as main transcript	c.1305A>G	p.Ala435Ala	synonymous_variant	3/3	1	NM_001080396.3	ENSP00000365080.1		B1AL88

Frequencies

GnomAD3 genomes

AF:

0.00396

AC:

603

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000555

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.00700

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00373

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00394

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00426

AC:

1070

AN:

251422

Hom.:

AF XY:

0.00458

AC XY:

623

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.00289

Gnomad ASJ exome

AF:

0.0242

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00542

Gnomad FIN exome

AF:

0.000324

Gnomad NFE exome

AF:

0.00428

Gnomad OTH exome

AF:

0.00897

GnomAD4 exome

AF:

0.00378

AC:

5528

AN:

1461842

Hom.:

Cov.:

AF XY:

0.00391

AC XY:

2844

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00320

Gnomad4 ASJ exome

AF:

0.0231

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00588

Gnomad4 FIN exome

AF:

0.000169

Gnomad4 NFE exome

AF:

0.00344

Gnomad4 OTH exome

AF:

0.00513

GnomAD4 genome

AF:

0.00396

AC:

603

AN:

152334

Hom.:

Cov.:

AF XY:

0.00400

AC XY:

298

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.000553

Gnomad4 AMR

AF:

0.00699

Gnomad4 ASJ

AF:

0.0294

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00373

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00394

Gnomad4 OTH

AF:

0.00663

Alfa

AF:

0.00490

Hom.:

Bravo

AF:

0.00457

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.00632

EpiControl

AF:

0.00717

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

NALF1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.038

DANN

Benign

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over