Genetic Variant ENSG00000299769:n.282+6562T>C (chr6-32420932-T-C) – 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+6562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,136 control chromosomes in the GnomAD database, including 1,537 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 ( 1537 hom., cov: 32)

Consequence

ENSG00000299769
ENST00000766247.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.561

Publications

27 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=-0.98).

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+6562T>C		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1 link	n.287-4436T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19782

AN:

152018

Hom.:

1537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0765

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.0888

Gnomad EAS

AF:

0.0390

Gnomad SAS

AF:

0.0462

Gnomad FIN

AF:

0.205

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.130

AC:

19788

AN:

152136

Hom.:

1537

Cov.:

AF XY:

0.127

AC XY:

9446

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.0767

AC:

3183

AN:

41506

American (AMR)

AF:

0.112

AC:

1717

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0888

AC:

308

AN:

3470

East Asian (EAS)

AF:

0.0389

AC:

201

AN:

5172

South Asian (SAS)

AF:

0.0456

AC:

220

AN:

4826

European-Finnish (FIN)

AF:

0.205

AC:

2168

AN:

10580

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11621

AN:

67974

Other (OTH)

AF:

0.123

AC:

260

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

874

1749

2623

3498

4372

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.149

Hom.:

2192

Bravo

AF:

0.122

Asia WGS

AF:

0.0570

AC:

199

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.0

(source)

DANN

Benign

0.48

PhyloP100

-0.56

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