Genetic Variant ENSG00000243296:n.51+13635G>C (chr3-99345087-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715235.1(ENSG00000243296):n.51+13635G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,934 control chromosomes in the GnomAD database, including 2,398 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 0.16 ( 2398 hom., cov: 32)

Consequence

ENSG00000243296
ENST00000715235.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.275

Publications

2 publications found

Variant links:

Genes affected

ENSG00000243296 (HGNC:):

ENSG00000243296 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 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
ENSG00000243296	ENST00000715235.1 link	n.51+13635G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23824

AN:

151816

Hom.:

2394

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0575

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.0775

Gnomad EAS

AF:

0.0178

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.163

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

GnomAD4 genome

AF:

0.157

AC:

23836

AN:

151934

Hom.:

2398

Cov.:

AF XY:

0.154

AC XY:

11424

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.0574

AC:

2379

AN:

41466

American (AMR)

AF:

0.192

AC:

2929

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.0775

AC:

269

AN:

3470

East Asian (EAS)

AF:

0.0178

AC:

AN:

5168

South Asian (SAS)

AF:

0.122

AC:

587

AN:

4804

European-Finnish (FIN)

AF:

0.208

AC:

2189

AN:

10518

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.218

AC:

14795

AN:

67944

Other (OTH)

AF:

0.162

AC:

341

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

981

1962

2942

3923

4904

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.0914

Hom.:

147

Bravo

AF:

0.153

Asia WGS

AF:

0.0660

AC:

231

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

2.6

(source)

DANN

Benign

0.53

PhyloP100

0.28

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