Genetic Variant ENSG00000257239:n.472-48815C>T (chr12-41878740-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 ENST00000550874.1(ENSG00000257239):n.472-48815C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,922 control chromosomes in the GnomAD database, including 22,030 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 0.53 ( 22030 hom., cov: 32)

Consequence

ENSG00000257239
ENST00000550874.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.207

Publications

2 publications found

Variant links:

Genes affected

ENSG00000257239 (HGNC:):

ENSG00000257239 links:

Genome browser will be placed here

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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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
ENSG00000257239	ENST00000550874.1 link	n.472-48815C>T	intron_variant	Intron 1 of 1	3
ENSG00000257239	ENST00000824751.1 link	n.123-48815C>T	intron_variant	Intron 1 of 1
ENSG00000257239	ENST00000824752.1 link	n.244-16577C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80337

AN:

151804

Hom.:

22026

Cov.:

show subpopulations

Gnomad AFR

AF:

0.451

Gnomad AMI

AF:

0.588

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.446

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.553

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

GnomAD4 genome

AF:

0.529

AC:

80385

AN:

151922

Hom.:

22030

Cov.:

AF XY:

0.523

AC XY:

38870

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.450

AC:

18636

AN:

41394

American (AMR)

AF:

0.529

AC:

8081

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.594

AC:

2062

AN:

3472

East Asian (EAS)

AF:

0.202

AC:

1046

AN:

5172

South Asian (SAS)

AF:

0.446

AC:

2144

AN:

4806

European-Finnish (FIN)

AF:

0.588

AC:

6196

AN:

10546

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.594

AC:

40352

AN:

67940

Other (OTH)

AF:

0.553

AC:

1168

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1898

3797

5695

7594

9492

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

692

1384

2076

2768

3460

<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:

0.451

Hom.:

1705

Bravo

AF:

0.523

Asia WGS

AF:

0.385

AC:

1340

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.5

(source)

DANN

Benign

0.58

PhyloP100

0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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