Genetic Variant ENSG00000298145:n.148+1287G>A (chr13-106416281-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000753311.1(ENSG00000298145):n.148+1287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,132 control chromosomes in the GnomAD database, including 6,201 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 0.27 ( 6201 hom., cov: 33)

Consequence

ENSG00000298145
ENST00000753311.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.839

Publications

1 publications found

Variant links:

Genes affected

ENSG00000298145 (HGNC:):

ENSG00000298145 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298145	ENST00000753311.1 link	n.148+1287G>A	intron_variant	Intron 1 of 1
ENSG00000298164	ENST00000753443.1 link	n.267-1270C>T	intron_variant	Intron 2 of 2
ENSG00000298177	ENST00000753680.1 link	n.33+491G>A	intron_variant	Intron 1 of 1
ENSG00000298177	ENST00000753681.1 link	n.129+373G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41065

AN:

152016

Hom.:

6203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.393

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.298

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.296

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

GnomAD4 genome

AF:

0.270

AC:

41093

AN:

152132

Hom.:

6201

Cov.:

AF XY:

0.269

AC XY:

19987

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.392

AC:

16274

AN:

41498

American (AMR)

AF:

0.346

AC:

5282

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.243

AC:

842

AN:

3470

East Asian (EAS)

AF:

0.298

AC:

1544

AN:

5178

South Asian (SAS)

AF:

0.265

AC:

1276

AN:

4822

European-Finnish (FIN)

AF:

0.150

AC:

1585

AN:

10592

Middle Eastern (MID)

AF:

0.349

AC:

102

AN:

292

European-Non Finnish (NFE)

AF:

0.197

AC:

13415

AN:

67980

Other (OTH)

AF:

0.294

AC:

621

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1471

2943

4414

5886

7357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.228

Hom.:

6820

Bravo

AF:

0.293

Asia WGS

AF:

0.281

AC:

977

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

(source)

DANN

Benign

0.61

PhyloP100

0.84

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