Genetic Variant ENSG00000303469:n.139-4438C>T (chr17-78350041-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000794841.1(ENSG00000303469):n.139-4438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,000 control chromosomes in the GnomAD database, including 20,397 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 0.50 ( 20397 hom., cov: 31)

Consequence

ENSG00000303469
ENST00000794841.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0790

Publications

7 publications found

Variant links:

Genes affected

ENSG00000303469 (HGNC:):

ENSG00000303469 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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000303469	ENST00000794841.1 link	n.139-4438C>T	intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794842.1 link	n.135+3362C>T	intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794843.1 link	n.212+2395C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.505

AC:

76712

AN:

151882

Hom.:

20395

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.576

Gnomad ASJ

AF:

0.474

Gnomad EAS

AF:

0.582

Gnomad SAS

AF:

0.556

Gnomad FIN

AF:

0.602

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.507

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

GnomAD4 genome

AF:

0.505

AC:

76735

AN:

152000

Hom.:

20397

Cov.:

AF XY:

0.508

AC XY:

37721

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.326

AC:

13499

AN:

41462

American (AMR)

AF:

0.576

AC:

8803

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.474

AC:

1644

AN:

3468

East Asian (EAS)

AF:

0.582

AC:

3006

AN:

5168

South Asian (SAS)

AF:

0.556

AC:

2679

AN:

4816

European-Finnish (FIN)

AF:

0.602

AC:

6369

AN:

10580

Middle Eastern (MID)

AF:

0.592

AC:

174

AN:

294

European-Non Finnish (NFE)

AF:

0.574

AC:

39020

AN:

67926

Other (OTH)

AF:

0.509

AC:

1074

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1867

3733

5600

7466

9333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

676

1352

2028

2704

3380

<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:

0.545

Hom.:

29855

Bravo

AF:

0.494

Asia WGS

AF:

0.545

AC:

1894

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.3

(source)

DANN

Benign

0.75

PhyloP100

-0.079

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