Genetic Variant ENST00000687402.3:n.200-27167T>C (chr2-62380963-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 ENST00000687402.3(ENSG00000228541):n.200-27167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,842 control chromosomes in the GnomAD database, including 11,442 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 0.35 ( 11442 hom., cov: 31)

Consequence

ENSG00000228541
ENST00000687402.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.239

Publications

6 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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.200-27167T>C	intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000689590.2 link	n.199-82876T>C	intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000701158.1 link	n.198-45271T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

53648

AN:

151726

Hom.:

11398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.566

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.571

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.345

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

GnomAD4 genome

AF:

0.354

AC:

53751

AN:

151842

Hom.:

11442

Cov.:

AF XY:

0.355

AC XY:

26384

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.566

AC:

23410

AN:

41374

American (AMR)

AF:

0.389

AC:

5941

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

890

AN:

3470

East Asian (EAS)

AF:

0.571

AC:

2934

AN:

5136

South Asian (SAS)

AF:

0.458

AC:

2202

AN:

4804

European-Finnish (FIN)

AF:

0.165

AC:

1739

AN:

10570

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.229

AC:

15582

AN:

67920

Other (OTH)

AF:

0.351

AC:

740

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1543

3085

4628

6170

7713

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

494

988

1482

1976

2470

<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:

0.285

Hom.:

2739

Bravo

AF:

0.378

Asia WGS

AF:

0.531

AC:

1845

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.5

(source)

DANN

Benign

0.63

PhyloP100

0.24

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