Genetic Variant ENSG00000225258:n.225+2389G>A (chr2-180689841-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000429816.1(ENSG00000225258):n.225+2389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,008 control chromosomes in the GnomAD database, including 14,016 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 0.43 ( 14016 hom., cov: 32)

Consequence

ENSG00000225258
ENST00000429816.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.153

Publications

6 publications found

Variant links:

Genes affected

ENSG00000225258 (HGNC:):

ENSG00000225258 links:

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new If you want to explore the variant's impact on the transcript ENST00000429816.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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 (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225258	ENST00000429816.1	TSL:3	n.225+2389G>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64803

AN:

151890

Hom.:

13990

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.305

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.442

Gnomad OTH

AF:

0.421

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

GnomAD4 genome

AF:

0.427

AC:

64874

AN:

152008

Hom.:

14016

Cov.:

AF XY:

0.424

AC XY:

31475

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.453

AC:

18790

AN:

41454

American (AMR)

AF:

0.396

AC:

6041

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

1541

AN:

3470

East Asian (EAS)

AF:

0.308

AC:

1592

AN:

5172

South Asian (SAS)

AF:

0.424

AC:

2041

AN:

4810

European-Finnish (FIN)

AF:

0.333

AC:

3511

AN:

10558

Middle Eastern (MID)

AF:

0.452

AC:

132

AN:

292

European-Non Finnish (NFE)

AF:

0.442

AC:

30049

AN:

67962

Other (OTH)

AF:

0.427

AC:

900

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1876

3753

5629

7506

9382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

602

1204

1806

2408

3010

<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:

0.333

Hom.:

1152

Bravo

AF:

0.430

Asia WGS

AF:

0.438

AC:

1529

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.7

(source)

DANN

Benign

0.62

PhyloP100

0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over