Variant rs3750505 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000374016.5(DELEC1):n.902G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 925,834 control chromosomes in the GnomAD database, including 9,243 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 0.16 ( 2152 hom., cov: 31)

Exomes 𝑓: 0.12 ( 7091 hom. )

Consequence

DELEC1
ENST00000374016.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.672

Variant links:

Genes affected

DELEC1 (HGNC:):

DELEC1 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DELEC1	NR_163556.1 linkuse as main transcript	n.902G>A		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5 linkuse as main transcript	n.902G>A		non_coding_transcript_exon_variant	8/8	1
ENSG00000228714	ENST00000646338.1 linkuse as main transcript	n.276-76861C>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23806

AN:

151792

Hom.:

2151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.0600

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.125

AC:

96555

AN:

773924

Hom.:

7091

Cov.:

AF XY:

0.122

AC XY:

48158

AN XY:

394416

show subpopulations

Gnomad4 AFR exome

AF:

0.225

Gnomad4 AMR exome

AF:

0.148

Gnomad4 ASJ exome

AF:

0.0612

Gnomad4 EAS exome

AF:

0.296

Gnomad4 SAS exome

AF:

0.0868

Gnomad4 FIN exome

AF:

0.176

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.157

AC:

23828

AN:

151910

Hom.:

2152

Cov.:

AF XY:

0.159

AC XY:

11813

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.0600

Gnomad4 EAS

AF:

0.318

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.177

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.131

Alfa

AF:

0.131

Hom.:

353

Bravo

AF:

0.158

Asia WGS

AF:

0.216

AC:

750

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

1.5

DANN

Benign

0.54

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