Genetic Variant ENSG00000287784:n.84+9303T>C (chr3-127209087-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000654542.1(ENSG00000287784):n.84+9303T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,320 control chromosomes in the GnomAD database, including 979 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 0.10 ( 979 hom., cov: 33)

Consequence

ENSG00000287784
ENST00000654542.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

3 publications found

Variant links:

Genes affected

ENSG00000287784 (HGNC:):

ENSG00000287784 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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287784	ENST00000654542.1 link	n.84+9303T>C	intron_variant	Intron 1 of 1
ENSG00000287784	ENST00000827470.1 link	n.197-4775T>C	intron_variant	Intron 1 of 1
ENSG00000287784	ENST00000827471.1 link	n.215-4775T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15307

AN:

152202

Hom.:

976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0279

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.0865

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.0927

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.104

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

GnomAD4 genome

AF:

0.101

AC:

15334

AN:

152320

Hom.:

979

Cov.:

AF XY:

0.102

AC XY:

7559

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0280

AC:

1166

AN:

41582

American (AMR)

AF:

0.135

AC:

2065

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0865

AC:

300

AN:

3470

East Asian (EAS)

AF:

0.255

AC:

1323

AN:

5182

South Asian (SAS)

AF:

0.0936

AC:

452

AN:

4828

European-Finnish (FIN)

AF:

0.114

AC:

1214

AN:

10608

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.126

AC:

8538

AN:

68022

Other (OTH)

AF:

0.105

AC:

223

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

715

1430

2144

2859

3574

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.116

Hom.:

746

Bravo

AF:

0.102

Asia WGS

AF:

0.130

AC:

453

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

7.4

(source)

DANN

Benign

0.87

PhyloP100

-0.0070

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