Genetic Variant ENST00000668367.1:n.151+33873G>A (chr6-93450974-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000668367.1(ENSG00000287683):n.151+33873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 151,910 control chromosomes in the GnomAD database, including 683 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 0.085 ( 683 hom., cov: 31)

Consequence

ENSG00000287683
ENST00000668367.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.179

Publications

1 publications found

Variant links:

Genes affected

ENSG00000287683 (HGNC:):

ENSG00000287683 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377899	XR_001744262.2 link	n.1220+3338G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287683	ENST00000668367.1 link	n.151+33873G>A		intron_variant	Intron 1 of 4
ENSG00000287683	ENST00000776530.1 link	n.169+33873G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0854

AC:

12960

AN:

151794

Hom.:

683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0263

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0973

Gnomad ASJ

AF:

0.0309

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.0909

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.0717

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

GnomAD4 genome

AF:

0.0853

AC:

12957

AN:

151910

Hom.:

683

Cov.:

AF XY:

0.0872

AC XY:

6476

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.0263

AC:

1091

AN:

41484

American (AMR)

AF:

0.0971

AC:

1478

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.0309

AC:

107

AN:

3462

East Asian (EAS)

AF:

0.101

AC:

520

AN:

5136

South Asian (SAS)

AF:

0.0910

AC:

439

AN:

4824

European-Finnish (FIN)

AF:

0.147

AC:

1553

AN:

10570

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.111

AC:

7531

AN:

67906

Other (OTH)

AF:

0.0714

AC:

150

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

600

1199

1799

2398

2998

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.102

Hom.:

600

Bravo

AF:

0.0780

Asia WGS

AF:

0.0920

AC:

325

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.96

(source)

DANN

Benign

0.61

PhyloP100

-0.18

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