Genetic Variant ENSG00000298262:n.108-2254A>C (chr4-11083057-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000754158.1(ENSG00000298262):n.108-2254A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,194 control chromosomes in the GnomAD database, including 3,098 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 0.19 ( 3098 hom., cov: 32)

Consequence

ENSG00000298262
ENST00000754158.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.90

Publications

2 publications found

Variant links:

Genes affected

ENSG00000298262 (HGNC:):

ENSG00000298262 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298262	ENST00000754158.1 link	n.108-2254A>C	intron_variant	Intron 1 of 5
ENSG00000298262	ENST00000754159.1 link	n.494+16114A>C	intron_variant	Intron 1 of 3
ENSG00000298262	ENST00000754160.1 link	n.486+16114A>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28245

AN:

152076

Hom.:

3074

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.182

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.189

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

GnomAD4 genome

AF:

0.186

AC:

28325

AN:

152194

Hom.:

3098

Cov.:

AF XY:

0.188

AC XY:

14018

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.297

AC:

12309

AN:

41484

American (AMR)

AF:

0.183

AC:

2793

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

423

AN:

3470

East Asian (EAS)

AF:

0.147

AC:

763

AN:

5186

South Asian (SAS)

AF:

0.184

AC:

889

AN:

4828

European-Finnish (FIN)

AF:

0.169

AC:

1797

AN:

10614

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8679

AN:

68000

Other (OTH)

AF:

0.193

AC:

407

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1152

2304

3457

4609

5761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.127

Hom.:

708

Bravo

AF:

0.193

Asia WGS

AF:

0.196

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.6

(source)

DANN

Benign

0.71

PhyloP100

2.9

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