Genetic Variant ENSG00000236106:n.328+11580G>A (chr2-5753937-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000829845.1(ENSG00000236106):n.328+11580G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,212 control chromosomes in the GnomAD database, including 2,110 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 0.14 ( 2110 hom., cov: 33)

Consequence

ENSG00000236106
ENST00000829845.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.878

Publications

1 publications found

Variant links:

Genes affected

ENSG00000236106 (HGNC:):

ENSG00000236106 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000236106	ENST00000829845.1 link	n.328+11580G>A	intron_variant	Intron 2 of 2
ENSG00000236106	ENST00000829846.1 link	n.317+11580G>A	intron_variant	Intron 3 of 3
ENSG00000236106	ENST00000829848.1 link	n.298-4607G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21402

AN:

152094

Hom.:

2102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.168

Gnomad ASJ

AF:

0.0789

Gnomad EAS

AF:

0.453

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0887

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.0737

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.141

AC:

21441

AN:

152212

Hom.:

2110

Cov.:

AF XY:

0.144

AC XY:

10726

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.226

AC:

9368

AN:

41506

American (AMR)

AF:

0.169

AC:

2579

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0789

AC:

274

AN:

3472

East Asian (EAS)

AF:

0.453

AC:

2337

AN:

5162

South Asian (SAS)

AF:

0.120

AC:

580

AN:

4818

European-Finnish (FIN)

AF:

0.0887

AC:

942

AN:

10618

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0738

AC:

5018

AN:

68018

Other (OTH)

AF:

0.131

AC:

276

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

894

1789

2683

3578

4472

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.109

Hom.:

211

Bravo

AF:

0.152

Asia WGS

AF:

0.269

AC:

938

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

0.19

(source)

DANN

Benign

0.29

PhyloP100

-0.88

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