Genetic Variant ENSG00000258235:n.119-1255A>G (chr12-72814958-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000547563.2(ENSG00000258235):n.119-1255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,030 control chromosomes in the GnomAD database, including 7,422 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 0.30 ( 7422 hom., cov: 32)

Consequence

ENSG00000258235
ENST00000547563.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.968

Publications

1 publications found

Variant links:

Genes affected

ENSG00000258235 (HGNC:):

ENSG00000258235 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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
ENSG00000258235	ENST00000547563.2 link	n.119-1255A>G	intron_variant	Intron 1 of 6	3
ENSG00000258235	ENST00000785613.1 link	n.97-1255A>G	intron_variant	Intron 1 of 7
ENSG00000258235	ENST00000785614.1 link	n.127-1255A>G	intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45916

AN:

151912

Hom.:

7405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.261

Gnomad OTH

AF:

0.282

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

GnomAD4 genome

AF:

0.302

AC:

45973

AN:

152030

Hom.:

7422

Cov.:

AF XY:

0.298

AC XY:

22150

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.416

AC:

17224

AN:

41434

American (AMR)

AF:

0.306

AC:

4675

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

1143

AN:

3468

East Asian (EAS)

AF:

0.142

AC:

736

AN:

5176

South Asian (SAS)

AF:

0.283

AC:

1360

AN:

4806

European-Finnish (FIN)

AF:

0.207

AC:

2186

AN:

10572

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.261

AC:

17738

AN:

67988

Other (OTH)

AF:

0.279

AC:

590

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1593

3187

4780

6374

7967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

444

888

1332

1776

2220

<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:

0.278

Hom.:

1037

Bravo

AF:

0.314

Asia WGS

AF:

0.238

AC:

831

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

(source)

DANN

Benign

0.23

PhyloP100

-0.97

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