Genetic Variant ENST00000640307.1:n.433-1492G>T (chr9-23664509-C-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000640307.1(ENSG00000283982):n.433-1492G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0000074 ( 0 hom., cov: 20)

Consequence

ENSG00000283982
ENST00000640307.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.121

Publications

1 publications found

Variant links:

Genes affected

ENSG00000283982 (HGNC:):

ENSG00000283982 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929563	NR_121602.1 link	n.445-1492G>T		intron_variant	Intron 3 of 27

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000283982	ENST00000640307.1 link	n.433-1492G>T	intron_variant	Intron 3 of 27	1
ENSG00000283982	ENST00000804428.1 link	n.352+7220G>T	intron_variant	Intron 2 of 3
ENSG00000283982	ENST00000804429.1 link	n.197+7780G>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00000739

AC:

AN:

135392

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000153

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.00000738

AC:

AN:

135424

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

65074

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33558

American (AMR)

AF:

0.00

AC:

AN:

13666

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3390

East Asian (EAS)

AF:

0.00

AC:

AN:

4596

South Asian (SAS)

AF:

0.00

AC:

AN:

4304

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7766

Middle Eastern (MID)

AF:

0.00

AC:

AN:

248

European-Non Finnish (NFE)

AF:

0.0000153

AC:

AN:

65158

Other (OTH)

AF:

0.00

AC:

AN:

1876

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

2537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.5

(source)

DANN

Benign

0.30

PhyloP100

-0.12

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