Genetic Variant ENSG00000259283:n.216-1565C>T (chr16-55268359-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 ENST00000558730.2(ENSG00000259283):n.216-1565C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,062 control chromosomes in the GnomAD database, including 2,032 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 0.15 ( 2032 hom., cov: 32)

Consequence

ENSG00000259283
ENST00000558730.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0410

Publications

5 publications found

Variant links:

Genes affected

ENSG00000259283 (HGNC:):

ENSG00000259283 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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
ENSG00000259283	ENST00000558730.2 link	n.216-1565C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23182

AN:

151944

Hom.:

2014

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.0846

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.158

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

GnomAD4 genome

AF:

0.153

AC:

23238

AN:

152062

Hom.:

2032

Cov.:

AF XY:

0.152

AC XY:

11312

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.199

AC:

8250

AN:

41450

American (AMR)

AF:

0.214

AC:

3276

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

448

AN:

3470

East Asian (EAS)

AF:

0.306

AC:

1576

AN:

5158

South Asian (SAS)

AF:

0.103

AC:

496

AN:

4816

European-Finnish (FIN)

AF:

0.104

AC:

1104

AN:

10580

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7608

AN:

67988

Other (OTH)

AF:

0.164

AC:

347

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1004

2008

3011

4015

5019

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.133

Hom.:

2271

Bravo

AF:

0.167

Asia WGS

AF:

0.249

AC:

862

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.94

(source)

DANN

Benign

0.57

PhyloP100

-0.041

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