Genetic Variant ENSG00000299588:n.413+6124T>C (chr9-101748176-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000764873.1(ENSG00000299588):n.413+6124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,040 control chromosomes in the GnomAD database, including 804 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 0.071 ( 804 hom., cov: 32)

Consequence

ENSG00000299588
ENST00000764873.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.402

Publications

2 publications found

Variant links:

Genes affected

ENSG00000299588 (HGNC:):

ENSG00000299588 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299588	ENST00000764873.1 link	n.413+6124T>C	intron_variant	Intron 4 of 4
ENSG00000299588	ENST00000764874.1 link	n.247+6124T>C	intron_variant	Intron 3 of 3
ENSG00000299588	ENST00000764876.1 link	n.248+6124T>C	intron_variant	Intron 3 of 3
ENSG00000299588	ENST00000764877.1 link	n.262+6124T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0705

AC:

10716

AN:

151922

Hom.:

802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0400

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.0143

Gnomad SAS

AF:

0.0294

Gnomad FIN

AF:

0.0278

Gnomad MID

AF:

0.0732

Gnomad NFE

AF:

0.0210

Gnomad OTH

AF:

0.0595

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

GnomAD4 genome

AF:

0.0706

AC:

10739

AN:

152040

Hom.:

804

Cov.:

AF XY:

0.0700

AC XY:

5202

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.192

AC:

7978

AN:

41490

American (AMR)

AF:

0.0399

AC:

608

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.0173

AC:

AN:

3460

East Asian (EAS)

AF:

0.0143

AC:

AN:

5168

South Asian (SAS)

AF:

0.0298

AC:

144

AN:

4832

European-Finnish (FIN)

AF:

0.0278

AC:

295

AN:

10610

Middle Eastern (MID)

AF:

0.0719

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0210

AC:

1424

AN:

67924

Other (OTH)

AF:

0.0641

AC:

135

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

468

937

1405

1874

2342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0847

Hom.:

493

Bravo

AF:

0.0759

Asia WGS

AF:

0.0400

AC:

140

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.78

(source)

DANN

Benign

0.47

PhyloP100

-0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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