Variant chr5-119020720-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_134249.1(DMXL1-DT):n.122-480G>A variant causes a intron, non coding transcript 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
NR_134249.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.61

Variant links:

Genes affected

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

DMXL1-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DMXL1-DT	NR_134249.1 linkuse as main transcript	n.122-480G>A		intron_variant, non_coding_transcript_variant
DMXL1-DT	NR_134250.1 linkuse as main transcript	n.86-480G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
DMXL1-DT	ENST00000504820.2 linkuse as main transcript	n.98-480G>A	intron_variant, non_coding_transcript_variant	4
DMXL1-DT	ENST00000506486.5 linkuse as main transcript	n.129-480G>A	intron_variant, non_coding_transcript_variant	3
DMXL1-DT	ENST00000510128.1 linkuse as main transcript	n.57-480G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

16911

AN:

151166

Hom.:

1012

Cov.:

show subpopulations

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.:

AF XY:

0.111

AC XY:

8224

AN XY:

73886

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.0860

Gnomad4 ASJ

AF:

0.111

Gnomad4 EAS

AF:

0.0208

Gnomad4 SAS

AF:

0.0929

Gnomad4 FIN

AF:

0.131

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.112

Alfa

AF:

0.0537

Hom.:

Bravo

AF:

0.112

Asia WGS

AF:

0.0640

AC:

223

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.11

DANN

Benign

0.50

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over