Genetic Variant ENST00000765578.1:n.660+3701G>C (chr8-8719829-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000765578.1(ENSG00000254367):n.660+3701G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,184 control chromosomes in the GnomAD database, including 2,065 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 0.15 ( 2065 hom., cov: 33)

Consequence

ENSG00000254367
ENST00000765578.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.371

Publications

2 publications found

Variant links:

Genes affected

ENSG00000254367 (HGNC:):

ENSG00000254367 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254367	ENST00000765578.1 link	n.660+3701G>C		intron_variant	Intron 3 of 3
ENSG00000254367	ENST00000765579.1 link	n.741-299G>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23073

AN:

152066

Hom.:

2067

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.0768

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.0757

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.149

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

GnomAD4 genome

AF:

0.152

AC:

23088

AN:

152184

Hom.:

2065

Cov.:

AF XY:

0.151

AC XY:

11221

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.254

AC:

10517

AN:

41474

American (AMR)

AF:

0.118

AC:

1800

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

449

AN:

3470

East Asian (EAS)

AF:

0.110

AC:

570

AN:

5186

South Asian (SAS)

AF:

0.0751

AC:

363

AN:

4832

European-Finnish (FIN)

AF:

0.143

AC:

1514

AN:

10606

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.109

AC:

7430

AN:

68006

Other (OTH)

AF:

0.149

AC:

314

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

971

1943

2914

3886

4857

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<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:

0.128

Hom.:

181

Bravo

AF:

0.155

Asia WGS

AF:

0.112

AC:

392

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.0

(source)

DANN

Benign

0.69

PhyloP100

-0.37

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