Genetic Variant ENSG00000307816:n.694+5266T>C (chr6-28808540-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 ENST00000829044.1(ENSG00000307816):n.694+5266T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 152,064 control chromosomes in the GnomAD database, including 469 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 0.070 ( 469 hom., cov: 30)

Consequence

ENSG00000307816
ENST00000829044.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.547

Publications

11 publications found

Variant links:

Genes affected

ENSG00000307816 (HGNC:):

ENSG00000307816 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000307816	ENST00000829044.1 link	n.694+5266T>C	intron_variant	Intron 2 of 2
ENSG00000307816	ENST00000829045.1 link	n.403+5266T>C	intron_variant	Intron 4 of 4
ENSG00000307816	ENST00000829046.1 link	n.280+5266T>C	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0701

AC:

10647

AN:

151946

Hom.:

468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0815

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.0285

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.0398

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0897

Gnomad OTH

AF:

0.0489

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

GnomAD4 genome

AF:

0.0700

AC:

10651

AN:

152064

Hom.:

469

Cov.:

AF XY:

0.0642

AC XY:

4772

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.0814

AC:

3380

AN:

41498

American (AMR)

AF:

0.0284

AC:

434

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0262

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5098

South Asian (SAS)

AF:

0.00104

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0398

AC:

422

AN:

10606

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0896

AC:

6092

AN:

67974

Other (OTH)

AF:

0.0483

AC:

102

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

508

1016

1524

2032

2540

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0834

Hom.:

Bravo

AF:

0.0707

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.9

(source)

DANN

Benign

0.24

PhyloP100

-0.55

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