Genetic Variant ENSG00000287146:n.362+12593T>G (chr22-19304923-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000664918.1(ENSG00000287146):n.362+12593T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,006 control chromosomes in the GnomAD database, including 7,121 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 0.29 ( 7121 hom., cov: 31)

Consequence

ENSG00000287146
ENST00000664918.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

Publications

5 publications found

Variant links:

Genes affected

ENSG00000287146 (HGNC:):

ENSG00000287146 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105372859	XR_938000.3 link	n.384+12593T>G	intron_variant	Intron 1 of 4
LOC105372859	XR_938001.3 link	n.384+12593T>G	intron_variant	Intron 1 of 4
LOC105372859	XR_938002.3 link	n.384+12593T>G	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287146	ENST00000664918.1 link	n.362+12593T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44140

AN:

151888

Hom.:

7113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.439

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.265

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

GnomAD4 genome

AF:

0.291

AC:

44172

AN:

152006

Hom.:

7121

Cov.:

AF XY:

0.287

AC XY:

21311

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.439

AC:

18192

AN:

41434

American (AMR)

AF:

0.274

AC:

4183

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.200

AC:

695

AN:

3468

East Asian (EAS)

AF:

0.315

AC:

1629

AN:

5178

South Asian (SAS)

AF:

0.172

AC:

830

AN:

4816

European-Finnish (FIN)

AF:

0.219

AC:

2317

AN:

10576

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.228

AC:

15491

AN:

67968

Other (OTH)

AF:

0.261

AC:

550

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1548

3096

4645

6193

7741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<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:

0.259

Hom.:

2264

Bravo

AF:

0.303

Asia WGS

AF:

0.232

AC:

806

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.0

(source)

DANN

Benign

0.40

PhyloP100

0.055

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