rs670957

chr15-34797231-G-A

Variant summary

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

The NR_120329.1(GJD2-DT):n.300-13265G>A 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 0.447 in 151,988 control chromosomes in the GnomAD database, including 15,966 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 0.45 (15966 hom., cov: 32)
• Consequence: GJD2-DT NR_120329.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJD2-DT	NR_120329.1	n.300-13265G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJD2-DT	ENST00000671663.1	n.95-13265G>A		intron_variant, non_coding_transcript_variant
GJD2-DT	ENST00000503496.6	n.300-13265G>A		intron_variant, non_coding_transcript_variant		2
GJD2-DT	ENST00000661009.1	n.343+538G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67812 AN: 151868 Hom.: 15928 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.447 AC: 67900 AN: 151988 Hom.: 15966 Cov.: 32 AF XY: 0.444 AC XY: 33011 AN XY: 74308

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.424

Alfa AF: 0.402 Hom.: 10232

Bravo AF: 0.469

Asia WGS AF: 0.399 AC: 1386 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	3.7
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs670957; hg19: chr15-35089432;