Genetic Variant ENST00000690965.2:n.440+566C>T (chr3-12230699-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 ENST00000690965.2(ENSG00000288952):n.440+566C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,146 control chromosomes in the GnomAD database, including 6,098 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 0.27 ( 6098 hom., cov: 32)

Consequence

ENSG00000288952
ENST00000690965.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.212

Publications

7 publications found

Variant links:

Genes affected

ENSG00000288952 (HGNC:):

ENSG00000288952 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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
ENSG00000288952	ENST00000690965.2 link	n.440+566C>T		intron_variant	Intron 2 of 3
ENSG00000288952	ENST00000764008.1 link	n.443+566C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41462

AN:

152028

Hom.:

6089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.537

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.0339

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.295

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

GnomAD4 genome

AF:

0.273

AC:

41502

AN:

152146

Hom.:

6098

Cov.:

AF XY:

0.268

AC XY:

19971

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.224

AC:

9275

AN:

41496

American (AMR)

AF:

0.242

AC:

3699

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1407

AN:

3470

East Asian (EAS)

AF:

0.0341

AC:

177

AN:

5184

South Asian (SAS)

AF:

0.157

AC:

755

AN:

4824

European-Finnish (FIN)

AF:

0.295

AC:

3118

AN:

10578

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.322

AC:

21860

AN:

67990

Other (OTH)

AF:

0.296

AC:

624

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1546

3092

4637

6183

7729

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.313

Hom.:

13107

Bravo

AF:

0.271

Asia WGS

AF:

0.125

AC:

435

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.6

(source)

DANN

Benign

0.67

PhyloP100

-0.21

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