rs1322251

Variant names:

• chr9-111659722-C-T
• rs1322251
• ENST00000374294.3:c.337-7093C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004125.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC25-GNG10	NM_004125.4		c.337-7093C>T		intron	N/A	NP_004116.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC25-GNG10	ENST00000374294.3	TSL:2	c.337-7093C>T		intron	N/A	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

African (AFR) AF: 0.394 AC: 16353 AN: 41464

American (AMR) AF: 0.193 AC: 2945 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3470

East Asian (EAS) AF: 0.123 AC: 635 AN: 5178

South Asian (SAS) AF: 0.190 AC: 918 AN: 4824

European-Finnish (FIN) AF: 0.0821 AC: 870 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4248 AN: 68016

Other (OTH) AF: 0.163 AC: 345 AN: 2112

Alfa AF: 0.128 Hom.: 851

Bravo AF: 0.193

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.28
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1322251; hg19: chr9-114422002;