Genetic Variant ENST00000788926.1:n.267+3565T>G (chr4-68749255-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 ENST00000788926.1(ENSG00000302692):n.267+3565T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,060 control chromosomes in the GnomAD database, including 11,574 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 0.35 ( 11574 hom., cov: 32)

Consequence

ENSG00000302692
ENST00000788926.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770

Publications

1 publications found

Variant links:

Genes affected

ENSG00000302692 (HGNC:):

ENSG00000302692 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000302692	ENST00000788926.1 link	n.267+3565T>G	intron_variant	Intron 2 of 6
ENSG00000302692	ENST00000788927.1 link	n.60+14942T>G	intron_variant	Intron 1 of 1
ENSG00000302711	ENST00000789023.1 link	n.245+1447A>C	intron_variant	Intron 1 of 4
ENSG00000302711	ENST00000789024.1 link	n.155+1447A>C	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53706

AN:

151942

Hom.:

11543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.352

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

GnomAD4 genome

AF:

0.354

AC:

53809

AN:

152060

Hom.:

11574

Cov.:

AF XY:

0.358

AC XY:

26591

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.593

AC:

24584

AN:

41448

American (AMR)

AF:

0.449

AC:

6857

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

755

AN:

3472

East Asian (EAS)

AF:

0.244

AC:

1258

AN:

5164

South Asian (SAS)

AF:

0.168

AC:

810

AN:

4828

European-Finnish (FIN)

AF:

0.304

AC:

3220

AN:

10578

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.225

AC:

15269

AN:

67984

Other (OTH)

AF:

0.356

AC:

751

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1565

3129

4694

6258

7823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.171

Hom.:

410

Bravo

AF:

0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.7

(source)

DANN

Benign

0.46

PhyloP100

0.077

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