Variant rs4822466 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001084393.2(DDTL):c.285-1271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 266,120 control chromosomes in the GnomAD database, including 33,568 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 0.44 ( 16961 hom., cov: 32)

Exomes 𝑓: 0.53 ( 16607 hom. )

Consequence

DDTL
NM_001084393.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0320

Variant links:

Genes affected

DDTL (HGNC:33446): (D-dopachrome tautomerase like) Predicted to enable lyase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

DDTL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDTL	NM_001084393.2 linkuse as main transcript	c.285-1271G>A		intron_variant		ENST00000215770.6	NP_001077862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDTL	ENST00000215770.6 linkuse as main transcript	c.285-1271G>A		intron_variant		2	NM_001084393.2	ENSP00000215770	P1

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66360

AN:

151886

Hom.:

16949

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.609

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.461

Gnomad SAS

AF:

0.587

Gnomad FIN

AF:

0.610

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.443

GnomAD4 exome

AF:

0.528

AC:

60241

AN:

114116

Hom.:

16607

AF XY:

0.526

AC XY:

28794

AN XY:

54734

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.375

Gnomad4 ASJ exome

AF:

0.410

Gnomad4 EAS exome

AF:

0.464

Gnomad4 SAS exome

AF:

0.574

Gnomad4 FIN exome

AF:

0.597

Gnomad4 NFE exome

AF:

0.538

Gnomad4 OTH exome

AF:

0.502

GnomAD4 genome

AF:

0.437

AC:

66375

AN:

152004

Hom.:

16961

Cov.:

AF XY:

0.446

AC XY:

33109

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.504

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.461

Gnomad4 SAS

AF:

0.589

Gnomad4 FIN

AF:

0.610

Gnomad4 NFE

AF:

0.549

Gnomad4 OTH

AF:

0.443

Alfa

AF:

0.471

Hom.:

2737

Bravo

AF:

0.415

Asia WGS

AF:

0.524

AC:

1822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.1

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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