Genetic Variant NM_001412.4:c.408T>C (chrX-20130537-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001412.4(EIF1AX):c.408T>C(p.Asp136Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 1,184,719 control chromosomes in the GnomAD database, including 177 homozygotes. There are 1,345 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 93 hom., 686 hem., cov: 22)

Exomes 𝑓: 0.0024 ( 84 hom. 659 hem. )

Consequence

EIF1AX
NM_001412.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.04

Variant links:

Genes affected

EIF1AX (HGNC:3250): (eukaryotic translation initiation factor 1A X-linked) This gene encodes an essential eukaryotic translation initiation factor. The protein is required for the binding of the 43S complex (a 40S subunit, eIF2/GTP/Met-tRNAi and eIF3) to the 5' end of capped RNA. [provided by RefSeq, Jul 2008]

EIF1AX links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant X-20130537-A-G is Benign according to our data. Variant chrX-20130537-A-G is described in ClinVar as [Benign]. Clinvar id is 781548.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.04 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF1AX	NM_001412.4 link	c.408T>C	p.Asp136Asp	synonymous_variant	Exon 6 of 7	ENST00000379607.10	NP_001403.1	P47813

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF1AX	ENST00000379607.10 link	c.408T>C	p.Asp136Asp	synonymous_variant	Exon 6 of 7	1	NM_001412.4	ENSP00000368927.5		P47813
EIF1AX	ENST00000379593.1 link	c.324T>C	p.Asp108Asp	synonymous_variant	Exon 5 of 6	3		ENSP00000368912.1		X6RAC9

Frequencies

GnomAD3 genomes

AF:

0.0242

AC:

2671

AN:

110207

Hom.:

Cov.:

AF XY:

0.0206

AC XY:

669

AN XY:

32449

show subpopulations

Gnomad AFR

AF:

0.0844

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00906

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00422

Gnomad NFE

AF:

0.000189

Gnomad OTH

AF:

0.0128

GnomAD3 exomes

AF:

0.00644

AC:

1083

AN:

168118

Hom.:

AF XY:

0.00357

AC XY:

197

AN XY:

55232

show subpopulations

Gnomad AFR exome

AF:

0.0823

Gnomad AMR exome

AF:

0.00289

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000626

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000649

Gnomad OTH exome

AF:

0.00223

GnomAD4 exome

AF:

0.00241

AC:

2587

AN:

1074465

Hom.:

Cov.:

AF XY:

0.00192

AC XY:

659

AN XY:

343137

show subpopulations

Gnomad4 AFR exome

AF:

0.0837

Gnomad4 AMR exome

AF:

0.00387

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000980

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000617

Gnomad4 OTH exome

AF:

0.00569

GnomAD4 genome

AF:

0.0244

AC:

2689

AN:

110254

Hom.:

Cov.:

AF XY:

0.0211

AC XY:

686

AN XY:

32506

show subpopulations

Gnomad4 AFR

AF:

0.0848

Gnomad4 AMR

AF:

0.00904

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000189

Gnomad4 OTH

AF:

0.0127

Alfa

AF:

0.00781

Hom.:

Bravo

AF:

0.0276

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 30, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.0

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.8

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

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