chr15-34789493-CT-C

Variant names:

• chr15-34789493-CT-C
• rs34323254
• ENST00000503496.6:n.299+12063delT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000503496.6(GJD2-DT):​n.299+12063delT variant causes a intron 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 ENST00000503496.6 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:2
• Conservation: PhyloP100: -1.56
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

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+12063delT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GJD2-DT	ENST00000503496.6	TSL:2	n.299+12063delT		intron	N/A
	GJD2-DT	ENST00000558707.4	TSL:3	n.322-313delT		intron	N/A
	GJD2-DT	ENST00000671663.2		n.139-21002delT		intron	N/A

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

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 1 AN: 8

East Asian (EAS) AF: 0.111 AC: 6 AN: 54

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0758 AC: 5 AN: 66

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.182 AC: 54 AN: 296

Other (OTH) AF: 0.250 AC: 7 AN: 28

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

African (AFR) AF: 0.0986 AC: 4098 AN: 41554

American (AMR) AF: 0.141 AC: 2152 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 609 AN: 3472

East Asian (EAS) AF: 0.124 AC: 642 AN: 5184

South Asian (SAS) AF: 0.249 AC: 1202 AN: 4826

European-Finnish (FIN) AF: 0.121 AC: 1280 AN: 10606

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10202 AN: 68008

Other (OTH) AF: 0.159 AC: 335 AN: 2110

Alfa AF: 0.0141 Hom.: 45

Bravo AF: 0.132

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Dilated Cardiomyopathy, Dominant (1)
-	-	1	Hypertrophic cardiomyopathy (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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