Genetic Variant ENST00000770125.1:n.85-2132G>T (chr3-147379060-C-A) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000770125.1(ENSG00000300216):n.85-2132G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,132 control chromosomes in the GnomAD database, including 843 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 0.096 ( 843 hom., cov: 33)

Consequence

ENSG00000300216
ENST00000770125.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.33

Publications

7 publications found

Variant links:

Genes affected

ENSG00000300216 (HGNC:):

ENSG00000300216 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=-0.22).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000300216	ENST00000770125.1 link	n.85-2132G>T	intron_variant	Intron 1 of 1
ENSG00000300216	ENST00000770126.1 link	n.130-2132G>T	intron_variant	Intron 2 of 2
ENSG00000300216	ENST00000770127.1 link	n.67-2132G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0963

AC:

14636

AN:

152014

Hom.:

844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0323

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0853

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.0863

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

GnomAD4 genome

AF:

0.0962

AC:

14641

AN:

152132

Hom.:

843

Cov.:

AF XY:

0.0984

AC XY:

7319

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.0322

AC:

1338

AN:

41536

American (AMR)

AF:

0.0852

AC:

1303

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

405

AN:

3466

East Asian (EAS)

AF:

0.163

AC:

840

AN:

5152

South Asian (SAS)

AF:

0.125

AC:

599

AN:

4810

European-Finnish (FIN)

AF:

0.174

AC:

1834

AN:

10552

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.119

AC:

8099

AN:

68012

Other (OTH)

AF:

0.0868

AC:

183

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

674

1347

2021

2694

3368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.108

Hom.:

1624

Bravo

AF:

0.0869

Asia WGS

AF:

0.132

AC:

461

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.22

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

2.3

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