Genetic Variant ENSG00000257239:n.472-30346G>T (chr12-41860271-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000550874.1(ENSG00000257239):n.472-30346G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,200 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 0.14 ( 1513 hom., cov: 32)

Consequence

ENSG00000257239
ENST00000550874.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.486

Publications

1 publications found

Variant links:

Genes affected

ENSG00000257239 (HGNC:):

ENSG00000257239 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 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
ENSG00000257239	ENST00000550874.1 link	n.472-30346G>T		intron_variant	Intron 1 of 1	3
ENSG00000257239	ENST00000824751.1 link	n.123-30346G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21503

AN:

152080

Hom.:

1511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.172

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.153

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.135

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

GnomAD4 genome

AF:

0.141

AC:

21506

AN:

152200

Hom.:

1513

Cov.:

AF XY:

0.142

AC XY:

10586

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.140

AC:

5799

AN:

41532

American (AMR)

AF:

0.140

AC:

2138

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

449

AN:

3470

East Asian (EAS)

AF:

0.172

AC:

889

AN:

5172

South Asian (SAS)

AF:

0.174

AC:

840

AN:

4824

European-Finnish (FIN)

AF:

0.127

AC:

1349

AN:

10600

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9594

AN:

68004

Other (OTH)

AF:

0.133

AC:

280

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

953

1906

2860

3813

4766

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.136

Hom.:

2447

Bravo

AF:

0.141

Asia WGS

AF:

0.148

AC:

514

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

8.7

(source)

DANN

Benign

0.50

PhyloP100

0.49

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