Genetic Variant ENSG00000298511:n.167+5226G>A (chr15-79683407-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 ENST00000756109.1(ENSG00000298511):n.167+5226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,022 control chromosomes in the GnomAD database, including 4,981 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 0.25 ( 4981 hom., cov: 33)

Consequence

ENSG00000298511
ENST00000756109.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.329

Publications

3 publications found

Variant links:

Genes affected

ENSG00000298511 (HGNC:):

ENSG00000298511 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=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298511	ENST00000756109.1 link	n.167+5226G>A	intron_variant	Intron 2 of 3
ENSG00000298511	ENST00000756110.1 link	n.167+5226G>A	intron_variant	Intron 2 of 2
ENSG00000298511	ENST00000756111.1 link	n.159+5226G>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37639

AN:

151904

Hom.:

4974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.300

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.244

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

GnomAD4 genome

AF:

0.248

AC:

37677

AN:

152022

Hom.:

4981

Cov.:

AF XY:

0.243

AC XY:

18090

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.300

AC:

12439

AN:

41462

American (AMR)

AF:

0.201

AC:

3078

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1066

AN:

3460

East Asian (EAS)

AF:

0.449

AC:

2316

AN:

5160

South Asian (SAS)

AF:

0.272

AC:

1310

AN:

4820

European-Finnish (FIN)

AF:

0.113

AC:

1190

AN:

10566

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.226

AC:

15386

AN:

67956

Other (OTH)

AF:

0.248

AC:

523

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1449

2898

4347

5796

7245

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

392

784

1176

1568

1960

<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:

0.229

Hom.:

803

Bravo

AF:

0.255

Asia WGS

AF:

0.364

AC:

1265

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

9.0

(source)

DANN

Benign

0.51

PhyloP100

0.33

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