Genetic Variant ENSG00000296323:n.194+46536T>C (chr10-10042603-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.194+46536T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,226 control chromosomes in the GnomAD database, including 1,699 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 ( 1699 hom., cov: 32)

Consequence

ENSG00000296323
ENST00000738164.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.111

Publications

1 publications found

Variant links:

Genes affected

ENSG00000296323 (HGNC:):

ENSG00000296323 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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.194+46536T>C		intron_variant	Intron 2 of 8
ENSG00000296323	ENST00000738165.1 link	n.221+46536T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21191

AN:

152108

Hom.:

1699

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.0872

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.139

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

GnomAD4 genome

AF:

0.139

AC:

21207

AN:

152226

Hom.:

1699

Cov.:

AF XY:

0.138

AC XY:

10239

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.206

AC:

8534

AN:

41524

American (AMR)

AF:

0.0871

AC:

1333

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

766

AN:

3470

East Asian (EAS)

AF:

0.107

AC:

556

AN:

5178

South Asian (SAS)

AF:

0.149

AC:

719

AN:

4822

European-Finnish (FIN)

AF:

0.102

AC:

1086

AN:

10602

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.113

AC:

7673

AN:

68010

Other (OTH)

AF:

0.140

AC:

295

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

930

1861

2791

3722

4652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.125

Hom.:

2962

Bravo

AF:

0.141

Asia WGS

AF:

0.145

AC:

504

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.0

(source)

DANN

Benign

0.66

PhyloP100

0.11

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