rs893131

chr15-34798711-T-C

Variant summary

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

The NR_120329.1(GJD2-DT):n.300-11785T>C 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 0.186 in 152,150 control chromosomes in the GnomAD database, including 3,372 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 0.19 (3372 hom., cov: 33)
• Consequence: GJD2-DT NR_120329.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJD2-DT	NR_120329.1	n.300-11785T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJD2-DT	ENST00000671663.1	n.95-11785T>C		intron_variant, non_coding_transcript_variant
GJD2-DT	ENST00000503496.6	n.300-11785T>C		intron_variant, non_coding_transcript_variant		2
GJD2-DT	ENST00000661009.1	n.343+2018T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28285 AN: 152032 Hom.: 3361 Cov.: 33

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.186 AC: 28296 AN: 152150 Hom.: 3372 Cov.: 33 AF XY: 0.191 AC XY: 14215 AN XY: 74394

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.209

Alfa AF: 0.181 Hom.: 450

Bravo AF: 0.192

Asia WGS AF: 0.241 AC: 838 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	6.7
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs893131; hg19: chr15-35090912;