rs11952762

Variant names:

• chr5-119019856-A-G
• rs11952762
• ENST00000504820.2:n.261+221T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000504820.2(DMXL1-DT):​n.261+221T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,298 control chromosomes in the GnomAD database, including 90 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 0.031 (90 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: DMXL1-DT ENST00000504820.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 2 publications found

Genes affected

DMXL1-DT (HGNC:55568): (DMXL1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0305 (4648/152298) while in subpopulation NFE AF = 0.0478 (3249/68032). AF 95% confidence interval is 0.0464. There are 90 homozygotes in GnomAd4. There are 2084 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 90 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504820.2. 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
	DMXL1-DT	NR_134249.1		n.285+221T>C		intron	N/A
	DMXL1-DT	NR_134250.1		n.249+221T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMXL1-DT	ENST00000504820.2	TSL:4	n.261+221T>C		intron	N/A
	DMXL1-DT	ENST00000506486.5	TSL:3	n.292+221T>C		intron	N/A
	DMXL1-DT	ENST00000510128.2	TSL:3	n.*59T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4650 AN: 152180 Hom.: 90 Cov.: 32

Gnomad AFR AF: 0.00905

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0305 AC: 4648 AN: 152298 Hom.: 90 Cov.: 32 AF XY: 0.0280 AC XY: 2084 AN XY: 74460

African (AFR) AF: 0.00902 AC: 375 AN: 41576

American (AMR) AF: 0.0382 AC: 584 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4828

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3249 AN: 68032

Other (OTH) AF: 0.0331 AC: 70 AN: 2114

Alfa AF: 0.0431 Hom.: 244

Bravo AF: 0.0319

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.63
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11952762; hg19: chr5-118355551;