Genetic Variant ENSG00000296323:n.300-51452T>C (chr10-10235382-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 ENST00000738164.1(ENSG00000296323):n.300-51452T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,236 control chromosomes in the GnomAD database, including 2,027 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 0.14 ( 2027 hom., cov: 33)

Consequence

ENSG00000296323
ENST00000738164.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.970

Publications

2 publications found

Variant links:

Genes affected

ENSG00000296323 (HGNC:):

ENSG00000296323 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 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
ENSG00000296323	ENST00000738164.1 link	n.300-51452T>C		intron_variant	Intron 3 of 8
ENSG00000296323	ENST00000738165.1 link	n.327-51452T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22019

AN:

152118

Hom.:

2024

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0385

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.108

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.177

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

GnomAD4 genome

AF:

0.145

AC:

22021

AN:

152236

Hom.:

2027

Cov.:

AF XY:

0.145

AC XY:

10773

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0384

AC:

1596

AN:

41556

American (AMR)

AF:

0.181

AC:

2769

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.278

AC:

963

AN:

3466

East Asian (EAS)

AF:

0.108

AC:

559

AN:

5176

South Asian (SAS)

AF:

0.221

AC:

1067

AN:

4828

European-Finnish (FIN)

AF:

0.147

AC:

1554

AN:

10606

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.191

AC:

12992

AN:

67998

Other (OTH)

AF:

0.175

AC:

368

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

968

1936

2904

3872

4840

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.187

Hom.:

5403

Bravo

AF:

0.143

Asia WGS

AF:

0.169

AC:

586

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

1.1

(source)

DANN

Benign

0.63

PhyloP100

-0.97

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