15-34757586-A-G

Position:

• chr15-34757586-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

GJD2-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GJD2-DT	NR_120329.1	n.138+2365A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GJD2-DT	ENST00000503496.6	n.138+2365A>G		intron_variant		2
GJD2-DT	ENST00000558707.3	n.118+2365A>G		intron_variant		3
GJD2-DT	ENST00000671663.1	n.94+2365A>G		intron_variant
GJD2-DT	ENST00000693120.2	n.116+2365A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82594 AN: 151944 Hom.: 22612 Cov.: 32

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.: 32 AF XY: 0.544 AC XY: 40440 AN XY: 74330

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.552

Alfa AF: 0.546 Hom.: 30192

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
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752876; hg19: chr15-35049787;