Genetic Variant ENST00000503496.6:n.300-11785T>C (chr15-34798711-T-C) – 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.300-11785T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,150 control chromosomes in the GnomAD database, including 3,372 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 0.19 ( 3372 hom., cov: 33)

Consequence

GJD2-DT
ENST00000503496.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.372

Publications

4 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=-0.71).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJD2-DT	NR_120329.1 link	n.300-11785T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GJD2-DT	ENST00000503496.6 link	n.300-11785T>C	intron_variant	Intron 2 of 2	2
GJD2-DT	ENST00000661009.1 link	n.343+2018T>C	intron_variant	Intron 1 of 1
GJD2-DT	ENST00000671663.2 link	n.139-11785T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28285

AN:

152032

Hom.:

3361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0575

Gnomad AMI

AF:

0.337

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.265

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.178

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.211

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

GnomAD4 genome

AF:

0.186

AC:

28296

AN:

152150

Hom.:

3372

Cov.:

AF XY:

0.191

AC XY:

14215

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.0574

AC:

2384

AN:

41530

American (AMR)

AF:

0.362

AC:

5530

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

847

AN:

3472

East Asian (EAS)

AF:

0.265

AC:

1372

AN:

5178

South Asian (SAS)

AF:

0.218

AC:

1050

AN:

4822

European-Finnish (FIN)

AF:

0.224

AC:

2365

AN:

10576

Middle Eastern (MID)

AF:

0.171

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.205

AC:

13950

AN:

67982

Other (OTH)

AF:

0.209

AC:

441

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1130

2260

3390

4520

5650

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<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:

0.181

Hom.:

450

Bravo

AF:

0.192

Asia WGS

AF:

0.241

AC:

838

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

6.7

(source)

DANN

Benign

0.91

PhyloP100

-0.37

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