dbSNP rs11694911: ENSG00000298698:n.251+828C>T (chr2-10433072-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+828C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,606 control chromosomes in the GnomAD database, including 1,267 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 0.12 ( 1267 hom., cov: 34)

Consequence

ENSG00000298698
ENST00000757451.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.609

Publications

4 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298698	ENST00000757451.1 link	n.251+828C>T	intron_variant	Intron 1 of 1
ENSG00000298698	ENST00000757452.1 link	n.132+828C>T	intron_variant	Intron 1 of 2
ENSG00000298739	ENST00000757688.1 link	n.-170G>A	upstream_gene_variant
ENSG00000298739	ENST00000757689.1 link	n.-227G>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18412

AN:

151486

Hom.:

1265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0995

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.331

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.122

AC:

18421

AN:

151606

Hom.:

1267

Cov.:

AF XY:

0.126

AC XY:

9372

AN XY:

74120

show subpopulations

African (AFR)

AF:

0.0996

AC:

4075

AN:

40902

American (AMR)

AF:

0.118

AC:

1812

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

418

AN:

3470

East Asian (EAS)

AF:

0.330

AC:

1706

AN:

5164

South Asian (SAS)

AF:

0.180

AC:

869

AN:

4832

European-Finnish (FIN)

AF:

0.167

AC:

1773

AN:

10614

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7273

AN:

68016

Other (OTH)

AF:

0.115

AC:

242

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

873

1746

2618

3491

4364

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.113

Hom.:

3042

Bravo

AF:

0.115

Asia WGS

AF:

0.237

AC:

821

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.7

(source)

DANN

Benign

0.47

PhyloP100

-0.61

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