Genetic Variant ENSG00000257239:n.472-39303A>T (chr12-41869228-T-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.472-39303A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,010 control chromosomes in the GnomAD database, including 18,460 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 0.45 ( 18460 hom., cov: 31)

Consequence

ENSG00000257239
ENST00000550874.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.403

Publications

3 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 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.472-39303A>T	intron_variant	Intron 1 of 1	3
ENSG00000257239	ENST00000824751.1 link	n.123-39303A>T	intron_variant	Intron 1 of 1
ENSG00000257239	ENST00000824752.1 link	n.244-7065A>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.454

AC:

68946

AN:

151890

Hom.:

18457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.588

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.583

Gnomad EAS

AF:

0.202

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.495

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

GnomAD4 genome

AF:

0.454

AC:

68965

AN:

152010

Hom.:

18460

Cov.:

AF XY:

0.451

AC XY:

33529

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.179

AC:

7434

AN:

41472

American (AMR)

AF:

0.499

AC:

7622

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.583

AC:

2022

AN:

3466

East Asian (EAS)

AF:

0.201

AC:

1037

AN:

5150

South Asian (SAS)

AF:

0.453

AC:

2181

AN:

4814

European-Finnish (FIN)

AF:

0.590

AC:

6219

AN:

10546

Middle Eastern (MID)

AF:

0.558

AC:

164

AN:

294

European-Non Finnish (NFE)

AF:

0.599

AC:

40705

AN:

67964

Other (OTH)

AF:

0.495

AC:

1045

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1678

3355

5033

6710

8388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

616

1232

1848

2464

3080

<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:

0.527

Hom.:

2885

Bravo

AF:

0.436

Asia WGS

AF:

0.366

AC:

1274

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

0.97

(source)

DANN

Benign

0.55

PhyloP100

-0.40

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