Genetic Variant ENST00000766247.1:n.283-8992C>T (chr6-32425100-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000766247.1(ENSG00000299769):n.283-8992C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 152,236 control chromosomes in the GnomAD database, including 936 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 0.092 ( 936 hom., cov: 32)

Consequence

ENSG00000299769
ENST00000766247.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.431

Publications

39 publications found

Variant links:

Genes affected

ENSG00000299769 (HGNC:):

ENSG00000299769 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 (NFE) allele frequency at 95% confidence interval = 0.14 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
ENSG00000299769	ENST00000766247.1 link	n.283-8992C>T		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1 link	n.287-268C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0924

AC:

14055

AN:

152118

Hom.:

937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0231

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.0845

Gnomad ASJ

AF:

0.0841

Gnomad EAS

AF:

0.0162

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.0789

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

GnomAD4 genome

AF:

0.0923

AC:

14049

AN:

152236

Hom.:

936

Cov.:

AF XY:

0.0882

AC XY:

6564

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0230

AC:

956

AN:

41554

American (AMR)

AF:

0.0842

AC:

1288

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0841

AC:

292

AN:

3472

East Asian (EAS)

AF:

0.0162

AC:

AN:

5186

South Asian (SAS)

AF:

0.00394

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.139

AC:

1469

AN:

10578

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.142

AC:

9672

AN:

68004

Other (OTH)

AF:

0.0781

AC:

165

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

647

1293

1940

2586

3233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<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:

0.129

Hom.:

4632

Bravo

AF:

0.0867

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.9

(source)

DANN

Benign

0.69

PhyloP100

0.43

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