Genetic Variant ENSG00000299769:n.282+1711G>T (chr6-32416081-G-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.282+1711G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,112 control chromosomes in the GnomAD database, including 1,479 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 0.13 ( 1479 hom., cov: 32)

Consequence

ENSG00000299769
ENST00000766247.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Publications

31 publications found

Variant links:

Genes affected

ENSG00000299769 (HGNC:):

ENSG00000299769 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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.282+1711G>T		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1 link	n.286+1711G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19303

AN:

151994

Hom.:

1479

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0666

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.0893

Gnomad EAS

AF:

0.0397

Gnomad SAS

AF:

0.0462

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.127

AC:

19309

AN:

152112

Hom.:

1479

Cov.:

AF XY:

0.124

AC XY:

9210

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0668

AC:

2773

AN:

41530

American (AMR)

AF:

0.112

AC:

1708

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0893

AC:

310

AN:

3472

East Asian (EAS)

AF:

0.0396

AC:

205

AN:

5182

South Asian (SAS)

AF:

0.0456

AC:

220

AN:

4826

European-Finnish (FIN)

AF:

0.203

AC:

2140

AN:

10534

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11590

AN:

67950

Other (OTH)

AF:

0.121

AC:

255

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

852

1704

2555

3407

4259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.160

Hom.:

5411

Bravo

AF:

0.119

Asia WGS

AF:

0.0570

AC:

197

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

1.0

(source)

DANN

Benign

0.73

PhyloP100

-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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