Genetic Variant ENST00000673514.1:n.1365-8319G>C (chr4-33685038-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000673514.1(ENSG00000288321):n.1365-8319G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,800 control chromosomes in the GnomAD database, including 15,744 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 0.33 ( 15744 hom., cov: 32)

Consequence

ENSG00000288321
ENST00000673514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.937

Publications

8 publications found

Variant links:

Genes affected

ENSG00000288321 (HGNC:):

ENSG00000288321 links:

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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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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
ENSG00000288321	ENST00000673514.1 link	n.1365-8319G>C		intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes

AF:

0.329

AC:

49979

AN:

151682

Hom.:

15691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.0363

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.283

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

GnomAD4 genome

AF:

0.330

AC:

50089

AN:

151800

Hom.:

15744

Cov.:

AF XY:

0.328

AC XY:

24323

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.825

AC:

34182

AN:

41430

American (AMR)

AF:

0.266

AC:

4054

AN:

15220

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

521

AN:

3464

East Asian (EAS)

AF:

0.331

AC:

1699

AN:

5132

South Asian (SAS)

AF:

0.174

AC:

837

AN:

4806

European-Finnish (FIN)

AF:

0.117

AC:

1238

AN:

10558

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6874

AN:

67878

Other (OTH)

AF:

0.281

AC:

592

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

960

1919

2879

3838

4798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.0639

Hom.:

Bravo

AF:

0.361

Asia WGS

AF:

0.322

AC:

1119

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.34

(source)

DANN

Benign

0.30

PhyloP100

-0.94

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