Genetic Variant ENST00000591869.1:n.175+12837A>G (chr18-60759099-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000591869.1(ENSG00000267098):n.175+12837A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 152,112 control chromosomes in the GnomAD database, including 709 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 0.061 ( 709 hom., cov: 32)

Consequence

ENSG00000267098
ENST00000591869.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.741

Publications

1 publications found

Variant links:

Genes affected

ENSG00000267098 (HGNC:):

ENSG00000267098 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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
ENSG00000267098	ENST00000591869.1 link	n.175+12837A>G		intron_variant	Intron 4 of 7	4
ENSG00000267098	ENST00000655645.1 link	n.111+12837A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.0609

AC:

9257

AN:

151994

Hom.:

699

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.0395

Gnomad ASJ

AF:

0.0167

Gnomad EAS

AF:

0.0225

Gnomad SAS

AF:

0.0159

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0138

Gnomad OTH

AF:

0.0612

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

GnomAD4 genome

AF:

0.0612

AC:

9302

AN:

152112

Hom.:

709

Cov.:

AF XY:

0.0596

AC XY:

4432

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.177

AC:

7340

AN:

41516

American (AMR)

AF:

0.0393

AC:

599

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.0167

AC:

AN:

3468

East Asian (EAS)

AF:

0.0226

AC:

117

AN:

5182

South Asian (SAS)

AF:

0.0157

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00292

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0138

AC:

936

AN:

67944

Other (OTH)

AF:

0.0605

AC:

128

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

409

819

1228

1638

2047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0458

Hom.:

Bravo

AF:

0.0701

Asia WGS

AF:

0.0350

AC:

120

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.34

(source)

DANN

Benign

0.50

PhyloP100

-0.74

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