rs34323254

chr15-34789493-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NR_120329.1(GJD2-DT):n.299+12063del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,736 control chromosomes in the GnomAD database, including 1,558 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (1552 hom., cov: 30)
  • Exomes 𝑓: 0.16 (6 hom.)
• Consequence: GJD2-DT NR_120329.1 intron, non_coding_transcript
• Clinical Significance: Likely benign criteria provided, single submitter B:2
• Conservation: PhyloP100: -1.56

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-34789493-CT-C is Benign according to our data. Variant chr15-34789493-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 315672.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJD2-DT	NR_120329.1	n.299+12063del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJD2-DT	ENST00000671663.1	n.95-21002del		intron_variant, non_coding_transcript_variant
GJD2-DT	ENST00000503496.6	n.299+12063del		intron_variant, non_coding_transcript_variant		2
GJD2-DT	ENST00000558707.3	n.280-313del		intron_variant, non_coding_transcript_variant		3
GJD2-DT	ENST00000693120.2	n.117-313del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20779 AN: 152156 Hom.: 1548 Cov.: 30

Gnomad AFR AF: 0.0986

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.160 AC: 74 AN: 462 Hom.: 6 Cov.: 0 AF XY: 0.136 AC XY: 33 AN XY: 242

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.0758

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.137 AC: 20789 AN: 152274 Hom.: 1552 Cov.: 30 AF XY: 0.136 AC XY: 10120 AN XY: 74456

Gnomad4 AFR AF: 0.0986

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.159

Alfa AF: 0.0257 Hom.: 45

Bravo AF: 0.132

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

Dilated Cardiomyopathy, Dominant Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Hypertrophic cardiomyopathy Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs34323254; hg19: chr15-35081694; COSMIC: COSV51760541; COSMIC: COSV51760541;