Genetic Variant ENST00000439293.5:n.144-6434A>G (chr3-40320631-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000439293.5(EIF1B-AS1):n.144-6434A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,120 control chromosomes in the GnomAD database, including 19,000 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 0.47 ( 19000 hom., cov: 32)

Consequence

EIF1B-AS1
ENST00000439293.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.152

Publications

9 publications found

Variant links:

Genes affected

EIF1B-AS1 (HGNC:):

EIF1B-AS1 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EIF1B-AS1	ENST00000439293.5 link	n.144-6434A>G	intron_variant	Intron 2 of 2	4
EIF1B-AS1	ENST00000715680.1 link	n.307-19235A>G	intron_variant	Intron 3 of 4
EIF1B-AS1	ENST00000782695.1 link	n.397+5519A>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70720

AN:

152002

Hom.:

18996

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.523

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.615

Gnomad OTH

AF:

0.478

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.465

AC:

70745

AN:

152120

Hom.:

19000

Cov.:

AF XY:

0.462

AC XY:

34382

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.197

AC:

8174

AN:

41520

American (AMR)

AF:

0.523

AC:

7987

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

1775

AN:

3470

East Asian (EAS)

AF:

0.241

AC:

1250

AN:

5178

South Asian (SAS)

AF:

0.383

AC:

1850

AN:

4824

European-Finnish (FIN)

AF:

0.590

AC:

6229

AN:

10560

Middle Eastern (MID)

AF:

0.531

AC:

156

AN:

294

European-Non Finnish (NFE)

AF:

0.615

AC:

41839

AN:

67990

Other (OTH)

AF:

0.477

AC:

1006

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1706

3412

5118

6824

8530

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

620

1240

1860

2480

3100

<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:

0.562

Hom.:

45747

Bravo

AF:

0.449

Asia WGS

AF:

0.313

AC:

1089

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.0

(source)

DANN

Benign

0.82

PhyloP100

0.15

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over