dbSNP rs16844716: EEF1A1P44:n.248A>C (chr1-199387388-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430498.1(EEF1A1P44):n.248A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0246 in 192,330 control chromosomes in the GnomAD database, including 236 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 0.030 ( 226 hom., cov: 32)

Exomes 𝑓: 0.0045 ( 10 hom. )

Consequence

EEF1A1P44
ENST00000430498.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.52

Publications

6 publications found

Variant links:

Genes affected

EEF1A1P44 (HGNC:56201): (eukaryotic translation elongation factor 1 alpha 1 pseudogene 44)

EEF1A1P44 links:

LINC02789 (HGNC:54310): (long intergenic non-protein coding RNA 2789)

LINC02789 links:

Genome browser will be placed here

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=-0.55).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1A1P44		n.199387388A>C		intragenic_variant
LINC02789	NR_147896.1 link	n.310-3933A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1A1P44	ENST00000430498.1 link	n.248A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02789	ENST00000452199.1 link	n.310-3933A>C		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0298

AC:

4534

AN:

152088

Hom.:

224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0140

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.000956

Gnomad OTH

AF:

0.0225

GnomAD4 exome

AF:

0.00449

AC:

180

AN:

40124

Hom.:

Cov.:

AF XY:

0.00320

AC XY:

AN XY:

23754

show subpopulations

African (AFR)

AF:

0.106

AC:

135

AN:

1270

American (AMR)

AF:

0.00566

AC:

AN:

5654

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

546

East Asian (EAS)

AF:

0.00

AC:

AN:

2500

South Asian (SAS)

AF:

0.000437

AC:

AN:

4578

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000491

AC:

AN:

20352

Other (OTH)

AF:

0.000639

AC:

AN:

1564

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0298

AC:

4542

AN:

152206

Hom.:

226

Cov.:

AF XY:

0.0295

AC XY:

2192

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.101

AC:

4205

AN:

41524

American (AMR)

AF:

0.0140

AC:

214

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5168

South Asian (SAS)

AF:

0.000829

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10632

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000956

AC:

AN:

67988

Other (OTH)

AF:

0.0222

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

202

403

605

806

1008

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<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:

0.0151

Hom.:

177

Bravo

AF:

0.0344

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

3.6

(source)

DANN

Benign

0.81

PhyloP100

6.5

Splicing

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