Genetic Variant ENST00000782994.1:n.371-10387T>G (chr4-77835861-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000782994.1(ENSG00000289379):n.371-10387T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,192 control chromosomes in the GnomAD database, including 2,970 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 0.18 ( 2970 hom., cov: 32)

Consequence

ENSG00000289379
ENST00000782994.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

Publications

6 publications found

Variant links:

Genes affected

ENSG00000289379 (HGNC:):

ENSG00000289379 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289379	ENST00000782994.1 link	n.371-10387T>G	intron_variant	Intron 1 of 3
ENSG00000289379	ENST00000782995.1 link	n.364-10387T>G	intron_variant	Intron 1 of 2
ENSG00000289379	ENST00000782996.1 link	n.364-10387T>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

27942

AN:

152074

Hom.:

2969

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.0173

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.214

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

GnomAD4 genome

AF:

0.184

AC:

27955

AN:

152192

Hom.:

2970

Cov.:

AF XY:

0.182

AC XY:

13539

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.109

AC:

4524

AN:

41532

American (AMR)

AF:

0.190

AC:

2896

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

1203

AN:

3472

East Asian (EAS)

AF:

0.0171

AC:

AN:

5192

South Asian (SAS)

AF:

0.167

AC:

806

AN:

4830

European-Finnish (FIN)

AF:

0.238

AC:

2517

AN:

10592

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.224

AC:

15226

AN:

67978

Other (OTH)

AF:

0.213

AC:

451

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1152

2304

3455

4607

5759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.215

Hom.:

11800

Bravo

AF:

0.175

Asia WGS

AF:

0.0880

AC:

307

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.9

(source)

DANN

Benign

0.68

PhyloP100

1.2

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