Genetic Variant ENSG00000223727:n.537+3200C>A (chr3-3334100-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000420000.6(ENSG00000223727):n.537+3200C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,156 control chromosomes in the GnomAD database, including 1,513 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 0.081 ( 1513 hom., cov: 32)

Consequence

ENSG00000223727
ENST00000420000.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.304

Publications

3 publications found

Variant links:

Genes affected

ENSG00000223727 (HGNC:):

ENSG00000223727 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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
ENSG00000223727	ENST00000420000.6 link	n.537+3200C>A	intron_variant	Intron 4 of 4	4
ENSG00000223727	ENST00000451031.5 link	n.339+3200C>A	intron_variant	Intron 3 of 5	3
ENSG00000223727	ENST00000455703.1 link	n.396+3200C>A	intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0807

AC:

12272

AN:

152038

Hom.:

1506

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0345

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.0866

Gnomad SAS

AF:

0.0224

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00116

Gnomad OTH

AF:

0.0632

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

GnomAD4 genome

AF:

0.0809

AC:

12304

AN:

152156

Hom.:

1513

Cov.:

AF XY:

0.0783

AC XY:

5826

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.265

AC:

11000

AN:

41462

American (AMR)

AF:

0.0344

AC:

526

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.00144

AC:

AN:

3468

East Asian (EAS)

AF:

0.0861

AC:

445

AN:

5170

South Asian (SAS)

AF:

0.0226

AC:

109

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00116

AC:

AN:

68014

Other (OTH)

AF:

0.0634

AC:

134

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

490

980

1470

1960

2450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0334

Hom.:

1272

Bravo

AF:

0.0910

Asia WGS

AF:

0.0730

AC:

254

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.85

(source)

DANN

Benign

0.81

PhyloP100

-0.30

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