Variant rs2413775 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000560344.6(SLC28A2-AS1):n.1963A>T 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 0.617 in 424,826 control chromosomes in the GnomAD database, including 83,943 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 0.61 ( 29256 hom., cov: 33)

Exomes 𝑓: 0.62 ( 54687 hom. )

Consequence

SLC28A2-AS1
ENST00000560344.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Variant links:

Genes affected

SLC28A2-AS1 (HGNC:):

SLC28A2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A2-AS1	NR_120335.1 linkuse as main transcript	n.181-18A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
SLC28A2-AS1	ENST00000560344.6 linkuse as main transcript	n.1963A>T	non_coding_transcript_exon_variant	4/4	5
SLC28A2-AS1	ENST00000559003.5 linkuse as main transcript	n.244-18A>T	intron_variant		2
SLC28A2-AS1	ENST00000663463.1 linkuse as main transcript	n.56-9560A>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.611

AC:

92865

AN:

152058

Hom.:

29246

Cov.:

show subpopulations

Gnomad AFR

AF:

0.577

Gnomad AMI

AF:

0.784

Gnomad AMR

AF:

0.503

Gnomad ASJ

AF:

0.617

Gnomad EAS

AF:

0.193

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.631

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.685

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.621

AC:

169201

AN:

272650

Hom.:

54687

Cov.:

AF XY:

0.620

AC XY:

97245

AN XY:

156944

show subpopulations

Gnomad4 AFR exome

AF:

0.564

Gnomad4 AMR exome

AF:

0.392

Gnomad4 ASJ exome

AF:

0.624

Gnomad4 EAS exome

AF:

0.195

Gnomad4 SAS exome

AF:

0.587

Gnomad4 FIN exome

AF:

0.633

Gnomad4 NFE exome

AF:

0.684

Gnomad4 OTH exome

AF:

0.626

GnomAD4 genome

AF:

0.610

AC:

92897

AN:

152176

Hom.:

29256

Cov.:

AF XY:

0.605

AC XY:

45044

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.577

Gnomad4 AMR

AF:

0.502

Gnomad4 ASJ

AF:

0.617

Gnomad4 EAS

AF:

0.193

Gnomad4 SAS

AF:

0.570

Gnomad4 FIN

AF:

0.631

Gnomad4 NFE

AF:

0.685

Gnomad4 OTH

AF:

0.598

Alfa

AF:

0.632

Hom.:

3832

Bravo

AF:

0.596

Asia WGS

AF:

0.395

AC:

1378

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.78

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