Genetic Variant ENSG00000228541:n.199+27891A>G (chr2-62324337-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000687402.3(ENSG00000228541):n.199+27891A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,032 control chromosomes in the GnomAD database, including 25,346 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 0.57 ( 25346 hom., cov: 32)

Consequence

ENSG00000228541
ENST00000687402.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.51

Publications

96 publications found

Variant links:

Genes affected

ENSG00000228541 (HGNC:):

ENSG00000228541 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=-1.08).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000228541	ENST00000687402.3 link	n.199+27891A>G	intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000687773.2 link	n.199+27891A>G	intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000688476.3 link	n.202-21577A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87270

AN:

151914

Hom.:

25318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.492

Gnomad AMI

AF:

0.607

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.557

Gnomad EAS

AF:

0.557

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.639

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.567

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

GnomAD4 genome

AF:

0.575

AC:

87364

AN:

152032

Hom.:

25346

Cov.:

AF XY:

0.576

AC XY:

42845

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.492

AC:

20411

AN:

41448

American (AMR)

AF:

0.599

AC:

9151

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.557

AC:

1929

AN:

3466

East Asian (EAS)

AF:

0.557

AC:

2885

AN:

5176

South Asian (SAS)

AF:

0.566

AC:

2724

AN:

4810

European-Finnish (FIN)

AF:

0.639

AC:

6749

AN:

10568

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.612

AC:

41614

AN:

67966

Other (OTH)

AF:

0.571

AC:

1204

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1886

3773

5659

7546

9432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.601

Hom.:

126606

Bravo

AF:

0.569

Asia WGS

AF:

0.575

AC:

2000

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.61

(source)

DANN

Benign

0.11

PhyloP100

-1.5

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