chr10-110426390-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP5-DT	ENST00000770940.1	n.376-24424G>A		intron_variant	Intron 3 of 4
DUSP5-DT	ENST00000770941.1	n.381-23034G>A		intron_variant	Intron 3 of 4
DUSP5-DT	ENST00000770942.1	n.286-12216G>A		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs11195128; hg19: chr10-112186148;