14-35403720-G-A

Variant names:

• chr14-35403720-G-A
• rs1050851
• NM_020529.3:c.306C>T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_020529.3(NFKBIA):​c.306C>T​(p.Ala102Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,612,520 control chromosomes in the GnomAD database, including 36,461 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (2292 hom., cov: 31)
  • Exomes 𝑓: 0.21 (34169 hom.)
• Consequence: NFKBIA NM_020529.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: -0.194
• Publications: 33 publications found

Genes affected

NFKBIA (HGNC:7797): (NFKB inhibitor alpha) This gene encodes a member of the NF-kappa-B inhibitor family, which contain multiple ankrin repeat domains. The encoded protein interacts with REL dimers to inhibit NF-kappa-B/REL complexes which are involved in inflammatory responses. The encoded protein moves between the cytoplasm and the nucleus via a nuclear localization signal and CRM1-mediated nuclear export. Mutations in this gene have been found in ectodermal dysplasia anhidrotic with T-cell immunodeficiency autosomal dominant disease. [provided by RefSeq, Aug 2011]

NFKBIA Gene-Disease associations (from GenCC):

• ectodermal dysplasia and immunodeficiency 2

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• ectodermal dysplasia and immune deficiency

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000310246 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP6: Variant 14-35403720-G-A is Benign according to our data. Variant chr14-35403720-G-A is described in ClinVar as [Benign]. Clinvar id is 313115.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.194 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKBIA	NM_020529.3	c.306C>T	p.Ala102Ala	synonymous_variant	Exon 2 of 6	ENST00000216797.10	NP_065390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFKBIA	ENST00000216797.10	c.306C>T	p.Ala102Ala	synonymous_variant	Exon 2 of 6	1	NM_020529.3	ENSP00000216797.6

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23536 AN: 152012 Hom.: 2293 Cov.: 31

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.151

GnomAD2 exomes AF: 0.166 AC: 41483 AN: 250372 AF XY: 0.172

Gnomad AFR exome AF: 0.0533

Gnomad AMR exome AF: 0.0999

Gnomad ASJ exome AF: 0.188

Gnomad EAS exome AF: 0.0152

Gnomad FIN exome AF: 0.163

Gnomad NFE exome AF: 0.222

Gnomad OTH exome AF: 0.186

GnomAD4 exome AF: 0.209 AC: 305398 AN: 1460388 Hom.: 34169 Cov.: 32 AF XY: 0.208 AC XY: 151440 AN XY: 726512

African (AFR) AF: 0.0526 AC: 1761 AN: 33476

American (AMR) AF: 0.104 AC: 4647 AN: 44660

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 4986 AN: 26120

East Asian (EAS) AF: 0.0233 AC: 926 AN: 39692

South Asian (SAS) AF: 0.177 AC: 15277 AN: 86152

European-Finnish (FIN) AF: 0.169 AC: 9041 AN: 53378

Middle Eastern (MID) AF: 0.210 AC: 1208 AN: 5754

European-Non Finnish (NFE) AF: 0.230 AC: 255526 AN: 1110824

Other (OTH) AF: 0.199 AC: 12026 AN: 60332

GnomAD4 genome AF: 0.155 AC: 23530 AN: 152132 Hom.: 2292 Cov.: 31 AF XY: 0.149 AC XY: 11076 AN XY: 74362

African (AFR) AF: 0.0537 AC: 2229 AN: 41526

American (AMR) AF: 0.137 AC: 2091 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3470

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5162

South Asian (SAS) AF: 0.160 AC: 774 AN: 4826

European-Finnish (FIN) AF: 0.170 AC: 1802 AN: 10586

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15386 AN: 67954

Other (OTH) AF: 0.149 AC: 314 AN: 2106

Alfa AF: 0.196 Hom.: 5392

Bravo AF: 0.146

Asia WGS AF: 0.0820 AC: 288 AN: 3478

EpiCase AF: 0.222

EpiControl AF: 0.236

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Ectodermal dysplasia and immunodeficiency 2 Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Nov 25, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:2

Nov 12, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 32% of patients studied by a panel of primary immunodeficiencies. Number of patients: 31. Only high quality variants are reported. -

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided Benign:2

Jun 09, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	9.7
DANN	Benign	0.89
PhyloP100		-0.19
PromoterAI		-0.067	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1050851; hg19: chr14-35872926; COSMIC: COSV53751737; COSMIC: COSV53751737;