Genetic Variant ENST00000503496.6:n.138+2365A>G (chr15-34757586-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000503496.6(GJD2-DT):n.138+2365A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,062 control chromosomes in the GnomAD database, including 22,633 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 0.54 ( 22633 hom., cov: 32)

Consequence

GJD2-DT
ENST00000503496.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12

Publications

7 publications found

Variant links:

Genes affected

GJD2-DT (HGNC:55560): (GJD2 divergent transcript)

GJD2-DT 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJD2-DT	NR_120329.1 link	n.138+2365A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GJD2-DT	ENST00000503496.6 link	n.138+2365A>G	intron_variant	Intron 1 of 2	2
GJD2-DT	ENST00000558707.4 link	n.160+2365A>G	intron_variant	Intron 1 of 2	3
GJD2-DT	ENST00000671663.2 link	n.138+2365A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.544

AC:

82594

AN:

151944

Hom.:

22612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.530

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.563

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.638

Gnomad FIN

AF:

0.619

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.553

Gnomad OTH

AF:

0.549

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

GnomAD4 genome

AF:

0.544

AC:

82663

AN:

152062

Hom.:

22633

Cov.:

AF XY:

0.544

AC XY:

40440

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.530

AC:

21974

AN:

41474

American (AMR)

AF:

0.493

AC:

7531

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.563

AC:

1952

AN:

3466

East Asian (EAS)

AF:

0.427

AC:

2208

AN:

5172

South Asian (SAS)

AF:

0.638

AC:

3077

AN:

4826

European-Finnish (FIN)

AF:

0.619

AC:

6544

AN:

10564

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.553

AC:

37583

AN:

67972

Other (OTH)

AF:

0.552

AC:

1165

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1946

3892

5839

7785

9731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.544

Hom.:

41901

Bravo

AF:

0.531

Asia WGS

AF:

0.569

AC:

1979

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.034

(source)

DANN

Benign

0.48

PhyloP100

-2.1

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