rs1322251

Positions:

• chr9-111659722-C-T

Variant summary

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

The NM_004125.4(DNAJC25-GNG10):​c.337-7093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,168 control chromosomes in the GnomAD database, including 3,985 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 0.18 (3985 hom., cov: 33)
• Consequence: DNAJC25-GNG10 NM_004125.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

DNAJC25-GNG10 (HGNC:37501): (DNAJC25-GNG10 readthrough) This gene represents naturally-occurring mRNAs that are co-transcribed products of the neighboring DNAJC25 and GNG10 genes. These transcripts include the first exon of DNAJC25 and the last two exons of GNG10, resulting in a protein that combines the N-terminus of DNAJC25 and the C-terminus of GNG10. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC25-GNG10	NM_004125.4	c.337-7093C>T		intron_variant			NP_004116.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC25-GNG10	ENST00000374294.3	c.337-7093C>T		intron_variant		2		ENSP00000363412.3

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26772 AN: 152050 Hom.: 3955 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.177 AC: 26860 AN: 152168 Hom.: 3985 Cov.: 33 AF XY: 0.178 AC XY: 13237 AN XY: 74398

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.0625

Gnomad4 OTH AF: 0.163

Alfa AF: 0.120 Hom.: 440

Bravo AF: 0.193

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322251; hg19: chr9-114422002;