rs11952762

chr5-119019856-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_134249.1(DMXL1-DT):n.285+221T>C 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 0.0305 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 NR_134249.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 90 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DMXL1-DT	NR_134249.1	n.285+221T>C		intron_variant, non_coding_transcript_variant
DMXL1-DT	NR_134250.1	n.249+221T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DMXL1-DT	ENST00000504820.2	n.261+221T>C		intron_variant, non_coding_transcript_variant		4
DMXL1-DT	ENST00000506486.5	n.292+221T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.00902

Gnomad4 AMR AF: 0.0382

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0478

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0444 Hom.: 202

Bravo AF: 0.0319

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.85
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11952762; hg19: chr5-118355551;