Variant chr17-44852391-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004247.4(EFTUD2):c.2715+18G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,613,486 control chromosomes in the GnomAD database, including 1,116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 69 hom., cov: 31)

Exomes 𝑓: 0.035 ( 1047 hom. )

Consequence

EFTUD2
NM_004247.4 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.772

Variant links:

Genes affected

EFTUD2 (HGNC:30858): (elongation factor Tu GTP binding domain containing 2) This gene encodes a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Mutations in this gene are associated with mandibulofacial dysostosis with microcephaly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

EFTUD2 links:

EFTUD2 (HGNC:):

EFTUD2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 17-44852391-C-G is Benign according to our data. Variant chr17-44852391-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 259255.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-44852391-C-G is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0237 (3601/152190) while in subpopulation NFE AF= 0.0389 (2648/68002). AF 95% confidence interval is 0.0377. There are 69 homozygotes in gnomad4. There are 1608 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 3601 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
EFTUD2	NM_004247.4 linkuse as main transcript	c.2715+18G>C	intron_variant	ENST00000426333.7	NP_004238.3	Q15029-1B3KX19
EFTUD2	NM_001258353.2 linkuse as main transcript	c.2715+18G>C	intron_variant		NP_001245282.1	Q15029-1
EFTUD2	NM_001258354.2 linkuse as main transcript	c.2685+18G>C	intron_variant		NP_001245283.1	Q15029-3
EFTUD2	NM_001142605.2 linkuse as main transcript	c.2610+18G>C	intron_variant		NP_001136077.1	Q15029-2B3KX19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFTUD2	ENST00000426333.7 linkuse as main transcript	c.2715+18G>C		intron_variant		1	NM_004247.4	ENSP00000392094.1		Q15029-1

Frequencies

GnomAD3 genomes

AF:

0.0237

AC:

3598

AN:

152072

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00727

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0121

Gnomad ASJ

AF:

0.0479

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0220

Gnomad FIN

AF:

0.0140

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0389

Gnomad OTH

AF:

0.0196

GnomAD3 exomes

AF:

0.0256

AC:

6433

AN:

250992

Hom.:

126

AF XY:

0.0271

AC XY:

3674

AN XY:

135670

show subpopulations

Gnomad AFR exome

AF:

0.00659

Gnomad AMR exome

AF:

0.0107

Gnomad ASJ exome

AF:

0.0466

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0278

Gnomad FIN exome

AF:

0.0138

Gnomad NFE exome

AF:

0.0369

Gnomad OTH exome

AF:

0.0250

GnomAD4 exome

AF:

0.0350

AC:

51097

AN:

1461296

Hom.:

1047

Cov.:

AF XY:

0.0346

AC XY:

25164

AN XY:

726930

show subpopulations

Gnomad4 AFR exome

AF:

0.00499

Gnomad4 AMR exome

AF:

0.0115

Gnomad4 ASJ exome

AF:

0.0454

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0285

Gnomad4 FIN exome

AF:

0.0150

Gnomad4 NFE exome

AF:

0.0396

Gnomad4 OTH exome

AF:

0.0300

GnomAD4 genome

AF:

0.0237

AC:

3601

AN:

152190

Hom.:

Cov.:

AF XY:

0.0216

AC XY:

1608

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.00725

Gnomad4 AMR

AF:

0.0120

Gnomad4 ASJ

AF:

0.0479

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0222

Gnomad4 FIN

AF:

0.0140

Gnomad4 NFE

AF:

0.0389

Gnomad4 OTH

AF:

0.0194

Alfa

AF:

0.0164

Hom.:

Bravo

AF:

0.0223

Asia WGS

AF:

0.00779

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.2

DANN

Benign

0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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