Genetic Variant ENST00000506864.5:n.472-16260T>C (chr4-89675025-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 ENST00000506864.5(ENSG00000251095):n.472-16260T>C 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 152,138 control chromosomes in the GnomAD database, including 3,036 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 ( 3036 hom., cov: 31)

Consequence

ENSG00000251095
ENST00000506864.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.61

Publications

0 publications found

Variant links:

Genes affected

ENSG00000251095 (HGNC:):

ENSG00000251095 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000251095	ENST00000506864.5 link	n.472-16260T>C	intron_variant	Intron 3 of 3	4
ENSG00000251095	ENST00000507916.6 link	n.135-16260T>C	intron_variant	Intron 1 of 2	3
ENSG00000251095	ENST00000508021.5 link	n.327-16260T>C	intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23260

AN:

152022

Hom.:

3024

Cov.:

show subpopulations

Gnomad AFR

AF:

0.352

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0783

Gnomad ASJ

AF:

0.0640

Gnomad EAS

AF:

0.0551

Gnomad SAS

AF:

0.0878

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.0746

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.153

AC:

23299

AN:

152138

Hom.:

3036

Cov.:

AF XY:

0.152

AC XY:

11278

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.352

AC:

14592

AN:

41450

American (AMR)

AF:

0.0781

AC:

1195

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0640

AC:

222

AN:

3470

East Asian (EAS)

AF:

0.0554

AC:

286

AN:

5162

South Asian (SAS)

AF:

0.0871

AC:

420

AN:

4822

European-Finnish (FIN)

AF:

0.102

AC:

1086

AN:

10614

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0746

AC:

5074

AN:

68002

Other (OTH)

AF:

0.128

AC:

270

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

887

1775

2662

3550

4437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.0995

Hom.:

370

Bravo

AF:

0.160

Asia WGS

AF:

0.104

AC:

361

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.83

(source)

DANN

Benign

0.24

PhyloP100

-2.6

Mutation Taster

=100/0

polymorphism

(source)

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