Genetic Variant ENSG00000237689:n.*208A>G (chr22-16871334-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000442403.1(ENSG00000237689):n.*208A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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 0.49 ( 0 hom., cov: 50)

Failed GnomAD Quality Control

Consequence

ENSG00000237689
ENST00000442403.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

2 publications found

Variant links:

COSMIC-nc: COSV71365362

Genes affected

ENSG00000237689 (HGNC:):

ENSG00000237689 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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
ENSG00000237689	ENST00000442403.1 link	n.*208A>G		downstream_gene_variant		5
ENSG00000237689	ENST00000821830.1 link	n.*53A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.488

AC:

68527

AN:

140390

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.483

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.492

Gnomad EAS

AF:

0.487

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.486

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.486

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.488

AC:

68559

AN:

140458

Hom.:

Cov.:

AF XY:

0.487

AC XY:

33406

AN XY:

68626

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.479

AC:

17773

AN:

37122

American (AMR)

AF:

0.492

AC:

7050

AN:

14318

Ashkenazi Jewish (ASJ)

AF:

0.492

AC:

1579

AN:

3210

East Asian (EAS)

AF:

0.487

AC:

2298

AN:

4720

South Asian (SAS)

AF:

0.493

AC:

2242

AN:

4546

European-Finnish (FIN)

AF:

0.495

AC:

4991

AN:

10078

Middle Eastern (MID)

AF:

0.485

AC:

133

AN:

274

European-Non Finnish (NFE)

AF:

0.491

AC:

31156

AN:

63436

Other (OTH)

AF:

0.486

AC:

931

AN:

1914

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.377

Heterozygous variant carriers

2797

5594

8392

11189

13986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

826

1652

2478

3304

4130

<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:

0.480

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.7

(source)

DANN

Benign

0.65

PhyloP100

-1.8

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