Genetic Variant ENSG00000228560:n.228-23385A>G (chr1-159387894-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 ENST00000431862.1(ENSG00000228560):n.228-23385A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,048 control chromosomes in the GnomAD database, including 20,250 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 0.46 ( 20250 hom., cov: 32)

Consequence

ENSG00000228560
ENST00000431862.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

Publications

17 publications found

Variant links:

Genes affected

ENSG00000228560 (HGNC:):

ENSG00000228560 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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
ENSG00000228560	ENST00000431862.1 link	n.228-23385A>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70441

AN:

151930

Hom.:

20201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.820

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.347

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.400

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

GnomAD4 genome

AF:

0.464

AC:

70547

AN:

152048

Hom.:

20250

Cov.:

AF XY:

0.463

AC XY:

34400

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.821

AC:

34013

AN:

41452

American (AMR)

AF:

0.443

AC:

6758

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

916

AN:

3464

East Asian (EAS)

AF:

0.335

AC:

1732

AN:

5172

South Asian (SAS)

AF:

0.295

AC:

1421

AN:

4822

European-Finnish (FIN)

AF:

0.347

AC:

3673

AN:

10576

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20771

AN:

67978

Other (OTH)

AF:

0.400

AC:

844

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1571

3141

4712

6282

7853

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

588

1176

1764

2352

2940

<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:

0.360

Hom.:

23691

Bravo

AF:

0.487

Asia WGS

AF:

0.392

AC:

1363

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

0.93

(source)

DANN

Benign

0.41

PhyloP100

-2.2

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