Genetic Variant ENST00000438318.1:n.63-3265T>C (chr1-107990240-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

The ENST00000438318.1(VAV3-AS1):n.63-3265T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,252 control chromosomes in the GnomAD database, including 69,026 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 0.95 ( 69026 hom., cov: 31)

Consequence

VAV3-AS1
ENST00000438318.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.789

Publications

1 publications found

Variant links:

Genes affected

VAV3-AS1 (HGNC:40608): (VAV3 antisense RNA 1)

VAV3-AS1 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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAV3-AS1	NR_046653.1 link	n.63-3265T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
VAV3-AS1	ENST00000438318.1 link	n.63-3265T>C	intron_variant	Intron 1 of 2	2
VAV3-AS1	ENST00000715653.1 link	n.138+25736T>C	intron_variant	Intron 1 of 4
VAV3-AS1	ENST00000820014.1 link	n.134+25736T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.950

AC:

144475

AN:

152134

Hom.:

68997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.837

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.977

Gnomad ASJ

AF:

0.990

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.998

Gnomad FIN

AF:

0.999

Gnomad MID

AF:

0.956

Gnomad NFE

AF:

0.994

Gnomad OTH

AF:

0.959

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

GnomAD4 genome

AF:

0.949

AC:

144559

AN:

152252

Hom.:

69026

Cov.:

AF XY:

0.951

AC XY:

70819

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.836

AC:

34724

AN:

41530

American (AMR)

AF:

0.977

AC:

14933

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.990

AC:

3438

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5162

AN:

5162

South Asian (SAS)

AF:

0.998

AC:

4820

AN:

4828

European-Finnish (FIN)

AF:

0.999

AC:

10610

AN:

10616

Middle Eastern (MID)

AF:

0.959

AC:

282

AN:

294

European-Non Finnish (NFE)

AF:

0.994

AC:

67652

AN:

68036

Other (OTH)

AF:

0.959

AC:

2026

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

338

676

1015

1353

1691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.947

Hom.:

31733

Bravo

AF:

0.942

Asia WGS

AF:

0.986

AC:

3430

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.5

(source)

DANN

Benign

0.63

PhyloP100

0.79

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