15-34776108-C-T

Variant names:

• chr15-34776108-C-T
• rs543686
• ENST00000808238.1:n.324C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000808238.1(GJD2-DT):​n.324C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,058 control chromosomes in the GnomAD database, including 9,075 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 0.34 (9075 hom., cov: 33)
• Consequence: GJD2-DT ENST00000808238.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJD2-DT	NR_120329.1	n.139-1163C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GJD2-DT	ENST00000808238.1	n.324C>T		non_coding_transcript_exon_variant	Exon 2 of 2
GJD2-DT	ENST00000503496.6	n.139-1163C>T		intron_variant	Intron 1 of 2	2
GJD2-DT	ENST00000558707.4	n.161-1163C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51259 AN: 151940 Hom.: 9063 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.337 AC: 51313 AN: 152058 Hom.: 9075 Cov.: 33 AF XY: 0.333 AC XY: 24728 AN XY: 74320

African (AFR) AF: 0.377 AC: 15649 AN: 41482

American (AMR) AF: 0.249 AC: 3815 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3470

East Asian (EAS) AF: 0.102 AC: 530 AN: 5178

South Asian (SAS) AF: 0.176 AC: 846 AN: 4816

European-Finnish (FIN) AF: 0.403 AC: 4254 AN: 10548

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24293 AN: 67954

Other (OTH) AF: 0.308 AC: 652 AN: 2114

Alfa AF: 0.344 Hom.: 16418

Bravo AF: 0.328

Asia WGS AF: 0.181 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.5
DANN	Benign	0.68
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs543686; hg19: chr15-35068309;