Genetic Variant ENSG00000304556:n.83+5415A>G (chr16-20250080-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 ENST00000804517.1(ENSG00000304556):n.83+5415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,146 control chromosomes in the GnomAD database, including 5,781 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 0.24 ( 5781 hom., cov: 32)

Consequence

ENSG00000304556
ENST00000804517.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.103

Publications

4 publications found

Variant links:

Genes affected

ENSG00000304556 (HGNC:):

ENSG00000304556 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 (AFR) allele frequency at 95% confidence interval = 0.454 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
ENSG00000304556	ENST00000804517.1 link	n.83+5415A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35730

AN:

152028

Hom.:

5749

Cov.:

show subpopulations

Gnomad AFR

AF:

0.458

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.217

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.179

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

GnomAD4 genome

AF:

0.235

AC:

35821

AN:

152146

Hom.:

5781

Cov.:

AF XY:

0.236

AC XY:

17557

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.459

AC:

19039

AN:

41472

American (AMR)

AF:

0.187

AC:

2861

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

535

AN:

3466

East Asian (EAS)

AF:

0.244

AC:

1259

AN:

5170

South Asian (SAS)

AF:

0.115

AC:

556

AN:

4822

European-Finnish (FIN)

AF:

0.217

AC:

2297

AN:

10592

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8761

AN:

68012

Other (OTH)

AF:

0.178

AC:

377

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1222

2443

3665

4886

6108

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.130

Hom.:

866

Bravo

AF:

0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

(source)

DANN

Benign

0.49

PhyloP100

-0.10

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