5-119020720-C-T

Variant names:

• chr5-119020720-C-T
• rs111649495
• ENST00000504820.2:n.98-480G>A

Variant summary

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

The ENST00000504820.2(DMXL1-DT):​n.98-480G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 151,284 control chromosomes in the GnomAD database, including 1,011 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 0.11 (1011 hom., cov: 30)
• Consequence: DMXL1-DT ENST00000504820.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.61
• Publications: 5 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

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.122-480G>A		intron	N/A
	DMXL1-DT	NR_134250.1		n.86-480G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMXL1-DT	ENST00000504820.2	TSL:4	n.98-480G>A		intron	N/A
	DMXL1-DT	ENST00000506486.5	TSL:3	n.129-480G>A		intron	N/A
	DMXL1-DT	ENST00000510128.2	TSL:3	n.256-480G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16911 AN: 151166 Hom.: 1012 Cov.: 30

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.112 AC: 16932 AN: 151284 Hom.: 1011 Cov.: 30 AF XY: 0.111 AC XY: 8224 AN XY: 73886

African (AFR) AF: 0.140 AC: 5760 AN: 41206

American (AMR) AF: 0.0860 AC: 1305 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3458

East Asian (EAS) AF: 0.0208 AC: 107 AN: 5152

South Asian (SAS) AF: 0.0929 AC: 444 AN: 4780

European-Finnish (FIN) AF: 0.131 AC: 1364 AN: 10392

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7155 AN: 67810

Other (OTH) AF: 0.112 AC: 236 AN: 2100

Alfa AF: 0.0537 Hom.: 55

Bravo AF: 0.112

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.50
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs111649495; hg19: chr5-118356415;