Genetic Variant ENSG00000238282:n.41+12604G>C (chr20-4488282-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000419863.1(ENSG00000238282):n.41+12604G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,066 control chromosomes in the GnomAD database, including 2,931 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 0.17 ( 2931 hom., cov: 32)

Consequence

ENSG00000238282
ENST00000419863.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.202

Publications

1 publications found

Variant links:

Genes affected

ENSG00000238282 (HGNC:):

ENSG00000238282 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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
ENSG00000238282	ENST00000419863.1 link	n.41+12604G>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26401

AN:

151948

Hom.:

2935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.0891

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.169

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

GnomAD4 genome

AF:

0.174

AC:

26408

AN:

152066

Hom.:

2931

Cov.:

AF XY:

0.177

AC XY:

13145

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.211

AC:

8743

AN:

41460

American (AMR)

AF:

0.170

AC:

2595

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0891

AC:

309

AN:

3468

East Asian (EAS)

AF:

0.565

AC:

2911

AN:

5154

South Asian (SAS)

AF:

0.324

AC:

1562

AN:

4822

European-Finnish (FIN)

AF:

0.134

AC:

1411

AN:

10566

Middle Eastern (MID)

AF:

0.127

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.121

AC:

8225

AN:

67994

Other (OTH)

AF:

0.170

AC:

358

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1055

2110

3165

4220

5275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.0687

Hom.:

Bravo

AF:

0.178

Asia WGS

AF:

0.428

AC:

1483

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.6

(source)

DANN

Benign

0.72

PhyloP100

-0.20

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