Genetic Variant ENST00000761310.1:n.150+33672G>T (chr7-118799878-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000761310.1(ENSG00000299159):n.150+33672G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,018 control chromosomes in the GnomAD database, including 2,482 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 0.10 ( 2482 hom., cov: 32)

Consequence

ENSG00000299159
ENST00000761310.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.982

Publications

1 publications found

Variant links:

Genes affected

ENSG00000299159 (HGNC:):

ENSG00000299159 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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
ENSG00000299159	ENST00000761310.1 link	n.150+33672G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15859

AN:

151900

Hom.:

2473

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0441

Gnomad ASJ

AF:

0.00865

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0216

Gnomad FIN

AF:

0.0101

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00975

Gnomad OTH

AF:

0.0790

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

GnomAD4 genome

AF:

0.105

AC:

15895

AN:

152018

Hom.:

2482

Cov.:

AF XY:

0.101

AC XY:

7474

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.342

AC:

14143

AN:

41398

American (AMR)

AF:

0.0440

AC:

672

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00865

AC:

AN:

3470

East Asian (EAS)

AF:

0.000386

AC:

AN:

5186

South Asian (SAS)

AF:

0.0222

AC:

107

AN:

4812

European-Finnish (FIN)

AF:

0.0101

AC:

107

AN:

10580

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00974

AC:

662

AN:

67982

Other (OTH)

AF:

0.0782

AC:

165

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

571

1142

1713

2284

2855

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0792

Hom.:

237

Bravo

AF:

0.117

Asia WGS

AF:

0.0230

AC:

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.30

(source)

DANN

Benign

0.13

PhyloP100

-0.98

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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