rs670957

Variant names:

• chr15-34797231-G-A
• rs670957
• ENST00000503496.6:n.300-13265G>A

Variant summary

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

The ENST00000503496.6(GJD2-DT):​n.300-13265G>A variant causes a intron 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 ENST00000503496.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503496.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GJD2-DT	NR_120329.1		n.300-13265G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GJD2-DT	ENST00000503496.6	TSL:2	n.300-13265G>A		intron	N/A
	GJD2-DT	ENST00000661009.1		n.343+538G>A		intron	N/A
	GJD2-DT	ENST00000671663.2		n.139-13265G>A		intron	N/A

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

African (AFR) AF: 0.577 AC: 23921 AN: 41424

American (AMR) AF: 0.498 AC: 7601 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1157 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2379 AN: 5160

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4816

European-Finnish (FIN) AF: 0.345 AC: 3651 AN: 10572

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26101 AN: 67960

Other (OTH) AF: 0.424 AC: 894 AN: 2108

Alfa AF: 0.410 Hom.: 29701

Bravo AF: 0.469

Asia WGS AF: 0.399 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.39
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs670957; hg19: chr15-35089432;