Genetic Variant ENSG00000223727:n.537+32846C>T (chr3-3304454-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 ENST00000420000.6(ENSG00000223727):n.537+32846C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,896 control chromosomes in the GnomAD database, including 3,848 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 0.22 ( 3848 hom., cov: 32)

Consequence

ENSG00000223727
ENST00000420000.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.324

Publications

4 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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
ENSG00000223727	ENST00000420000.6 link	n.537+32846C>T		intron_variant	Intron 4 of 4	4
ENSG00000223727	ENST00000451031.5 link	n.339+32846C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

33673

AN:

151780

Hom.:

3840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.222

AC:

33700

AN:

151896

Hom.:

3848

Cov.:

AF XY:

0.221

AC XY:

16404

AN XY:

74192

show subpopulations

African (AFR)

AF:

0.186

AC:

7729

AN:

41472

American (AMR)

AF:

0.233

AC:

3547

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1140

AN:

3468

East Asian (EAS)

AF:

0.193

AC:

994

AN:

5156

South Asian (SAS)

AF:

0.250

AC:

1203

AN:

4804

European-Finnish (FIN)

AF:

0.197

AC:

2071

AN:

10538

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16207

AN:

67910

Other (OTH)

AF:

0.239

AC:

504

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1329

2659

3988

5318

6647

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.223

Hom.:

4302

Bravo

AF:

0.223

Asia WGS

AF:

0.200

AC:

698

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

(source)

DANN

Benign

0.63

PhyloP100

-0.32

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