10-110426390-C-T

Variant names:

• chr10-110426390-C-T
• rs11195128
• ENST00000770940.1:n.376-24424G>A

Variant summary

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

The ENST00000770940.1(DUSP5-DT):​n.376-24424G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 147,366 control chromosomes in the GnomAD database, including 5,894 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 0.27 (5894 hom., cov: 28)
• Consequence: DUSP5-DT ENST00000770940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 22 publications found

Genes affected

DUSP5-DT (HGNC:55154): (DUSP5 divergent transcript)

ENSG00000300364 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770940.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP5-DT	ENST00000770940.1		n.376-24424G>A		intron	N/A
	DUSP5-DT	ENST00000770941.1		n.381-23034G>A		intron	N/A
	DUSP5-DT	ENST00000770942.1		n.286-12216G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 40264 AN: 147252 Hom.: 5900 Cov.: 28

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.273 AC: 40248 AN: 147366 Hom.: 5894 Cov.: 28 AF XY: 0.273 AC XY: 19550 AN XY: 71636

African (AFR) AF: 0.179 AC: 7059 AN: 39466

American (AMR) AF: 0.224 AC: 3215 AN: 14342

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 966 AN: 3446

East Asian (EAS) AF: 0.146 AC: 723 AN: 4938

South Asian (SAS) AF: 0.183 AC: 854 AN: 4674

European-Finnish (FIN) AF: 0.396 AC: 3891 AN: 9832

Middle Eastern (MID) AF: 0.227 AC: 63 AN: 278

European-Non Finnish (NFE) AF: 0.334 AC: 22508 AN: 67440

Other (OTH) AF: 0.259 AC: 530 AN: 2048

Alfa AF: 0.306 Hom.: 31705

Bravo AF: 0.249

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.63
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11195128;

hg19: chr10-112186148;