Genetic Variant ENSG00000298698:n.251+4062C>T (chr2-10436306-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000757451.1(ENSG00000298698):n.251+4062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,246 control chromosomes in the GnomAD database, including 1,052 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 0.11 ( 1052 hom., cov: 34)

Consequence

ENSG00000298698
ENST00000757451.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.733

Publications

1 publications found

Variant links:

Genes affected

ENSG00000298698 (HGNC:):

ENSG00000298698 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 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
ENSG00000298698	ENST00000757451.1 link	n.251+4062C>T		intron_variant	Intron 1 of 1
ENSG00000298698	ENST00000757452.1 link	n.132+4062C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17042

AN:

152128

Hom.:

1053

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0731

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.0994

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.265

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.0979

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

GnomAD4 genome

AF:

0.112

AC:

17032

AN:

152246

Hom.:

1052

Cov.:

AF XY:

0.115

AC XY:

8524

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.0731

AC:

3038

AN:

41556

American (AMR)

AF:

0.0989

AC:

1513

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

381

AN:

3470

East Asian (EAS)

AF:

0.265

AC:

1366

AN:

5164

South Asian (SAS)

AF:

0.119

AC:

572

AN:

4826

European-Finnish (FIN)

AF:

0.181

AC:

1921

AN:

10600

Middle Eastern (MID)

AF:

0.144

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.114

AC:

7767

AN:

68012

Other (OTH)

AF:

0.0959

AC:

203

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

810

1621

2431

3242

4052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.116

Hom.:

134

Bravo

AF:

0.104

Asia WGS

AF:

0.186

AC:

645

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.0

(source)

DANN

Benign

0.48

PhyloP100

-0.73

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