Genetic Variant NM_001130053.5:c.-1+45C>T (chr8-143592602-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001130053.5(EEF1D):c.-1+45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 985,088 control chromosomes in the GnomAD database, including 340,890 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 0.73 ( 42087 hom., cov: 34)

Exomes 𝑓: 0.84 ( 298803 hom. )

Consequence

EEF1D
NM_001130053.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.584

Publications

12 publications found

Variant links:

Genes affected

EEF1D (HGNC:3211): (eukaryotic translation elongation factor 1 delta) This gene encodes a subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This subunit, delta, functions as guanine nucleotide exchange factor. It is reported that following HIV-1 infection, this subunit interacts with HIV-1 Tat. This interaction results in repression of translation of host cell proteins and enhanced translation of viral proteins. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. Related pseudogenes have been defined on chromosomes 1, 6, 7, 9, 11, 13, 17, 19.[provided by RefSeq, Aug 2010]

EEF1D links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1D	NM_001130053.5 link	c.-1+45C>T		intron_variant	Intron 2 of 9	ENST00000618139.4	NP_001123525.3	P29692-2D3DWK1B2RAR6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1D	ENST00000618139.4 link	c.-1+45C>T		intron_variant	Intron 2 of 9	5	NM_001130053.5	ENSP00000484536.2		P29692-2A0A087X1X7

Frequencies

GnomAD3 genomes

AF:

0.727

AC:

110544

AN:

152050

Hom.:

42080

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.820

Gnomad AMR

AF:

0.765

Gnomad ASJ

AF:

0.829

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.694

Gnomad FIN

AF:

0.827

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.851

Gnomad OTH

AF:

0.764

GnomAD4 exome

AF:

0.845

AC:

703583

AN:

832920

Hom.:

298803

Cov.:

AF XY:

0.845

AC XY:

325226

AN XY:

384666

show subpopulations

African (AFR)

AF:

0.492

AC:

7770

AN:

15778

American (AMR)

AF:

0.761

AC:

752

AN:

988

Ashkenazi Jewish (ASJ)

AF:

0.822

AC:

4237

AN:

5152

East Asian (EAS)

AF:

0.518

AC:

1880

AN:

3632

South Asian (SAS)

AF:

0.706

AC:

11624

AN:

16456

European-Finnish (FIN)

AF:

0.802

AC:

231

AN:

288

Middle Eastern (MID)

AF:

0.801

AC:

1299

AN:

1622

European-Non Finnish (NFE)

AF:

0.858

AC:

653631

AN:

761696

Other (OTH)

AF:

0.811

AC:

22159

AN:

27308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

5805

11610

17415

23220

29025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19778

39556

59334

79112

98890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.727

AC:

110585

AN:

152168

Hom.:

42087

Cov.:

AF XY:

0.724

AC XY:

53865

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.500

AC:

20755

AN:

41472

American (AMR)

AF:

0.765

AC:

11702

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.829

AC:

2879

AN:

3472

East Asian (EAS)

AF:

0.509

AC:

2634

AN:

5176

South Asian (SAS)

AF:

0.694

AC:

3348

AN:

4824

European-Finnish (FIN)

AF:

0.827

AC:

8765

AN:

10600

Middle Eastern (MID)

AF:

0.799

AC:

235

AN:

294

European-Non Finnish (NFE)

AF:

0.851

AC:

57901

AN:

68006

Other (OTH)

AF:

0.765

AC:

1618

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1406

2811

4217

5622

7028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

824

1648

2472

3296

4120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.779

Hom.:

5875

Bravo

AF:

0.712

Asia WGS

AF:

0.593

AC:

2065

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

0.58

PromoterAI

-0.0017

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over