dbSNP rs589759: GJD2-DT:n.299+11942C>T (chr15-34789373-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000503496.6(GJD2-DT):n.299+11942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 161,320 control chromosomes in the GnomAD database, including 40,551 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 38413 hom., cov: 32)

Exomes 𝑓: 0.67 ( 2138 hom. )

Consequence

GJD2-DT
ENST00000503496.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.706

Publications

7 publications found

Variant links:

Genes affected

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

GJD2-DT links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000503496.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 15-34789373-C-T is Benign according to our data. Variant chr15-34789373-C-T is described in ClinVar as Benign. ClinVar VariationId is 315668.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503496.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GJD2-DT	NR_120329.1		n.299+11942C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
GJD2-DT	ENST00000503496.6	TSL:2	n.299+11942C>T	intron	N/A
GJD2-DT	ENST00000558707.4	TSL:3	n.322-434C>T	intron	N/A
GJD2-DT	ENST00000671663.2		n.139-21123C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107549

AN:

151950

Hom.:

38365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.714

Gnomad AMI

AF:

0.751

Gnomad AMR

AF:

0.625

Gnomad ASJ

AF:

0.802

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.738

Gnomad FIN

AF:

0.718

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.712

GnomAD4 exome

AF:

0.670

AC:

6198

AN:

9252

Hom.:

2138

Cov.:

AF XY:

0.671

AC XY:

3273

AN XY:

4878

show subpopulations

African (AFR)

AF:

0.728

AC:

147

AN:

202

American (AMR)

AF:

0.625

AC:

100

AN:

160

Ashkenazi Jewish (ASJ)

AF:

0.785

AC:

193

AN:

246

East Asian (EAS)

AF:

0.421

AC:

528

AN:

1254

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.714

AC:

957

AN:

1340

Middle Eastern (MID)

AF:

0.850

AC:

AN:

European-Non Finnish (NFE)

AF:

0.704

AC:

3825

AN:

5432

Other (OTH)

AF:

0.711

AC:

351

AN:

494

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

173

260

346

433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

GnomAD4 genome

AF:

0.708

AC:

107650

AN:

152068

Hom.:

38413

Cov.:

AF XY:

0.703

AC XY:

52233

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.715

AC:

29641

AN:

41474

American (AMR)

AF:

0.626

AC:

9563

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.802

AC:

2785

AN:

3472

East Asian (EAS)

AF:

0.488

AC:

2519

AN:

5158

South Asian (SAS)

AF:

0.737

AC:

3552

AN:

4818

European-Finnish (FIN)

AF:

0.718

AC:

7579

AN:

10560

Middle Eastern (MID)

AF:

0.735

AC:

216

AN:

294

European-Non Finnish (NFE)

AF:

0.730

AC:

49604

AN:

67984

Other (OTH)

AF:

0.713

AC:

1506

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1597

3195

4792

6390

7987

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<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:

0.711

Hom.:

46353

Bravo

AF:

0.695

Asia WGS

AF:

0.647

AC:

2250

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Dilated cardiomyopathy 1R (1)

Hypertrophic cardiomyopathy 11 (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

6.7

(source)

DANN

Benign

0.70

PhyloP100

0.71

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over