chr15-34800842-G-T

Variant names:

• chr15-34800842-G-T
• rs1402861
• ENST00000503496.6:n.300-9654G>T

Variant summary

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

The ENST00000503496.6(GJD2-DT):​n.300-9654G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 151,578 control chromosomes in the GnomAD database, including 2,382 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 0.099 (2382 hom., cov: 28)
• Consequence: GJD2-DT ENST00000503496.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJD2-DT	NR_120329.1	n.300-9654G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GJD2-DT	ENST00000503496.6	n.300-9654G>T		intron_variant	Intron 2 of 2	2
GJD2-DT	ENST00000661009.1	n.343+4149G>T		intron_variant	Intron 1 of 1
GJD2-DT	ENST00000671663.1	n.95-9654G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14901 AN: 151458 Hom.: 2376 Cov.: 28

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0414

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00437

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.00324

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0986 AC: 14941 AN: 151578 Hom.: 2382 Cov.: 28 AF XY: 0.0943 AC XY: 6985 AN XY: 74080

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.0413

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00416

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00321

Gnomad4 OTH AF: 0.0802

Alfa AF: 0.0760 Hom.: 226

Bravo AF: 0.112

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402861; hg19: chr15-35093043;