Variant rs2353576 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000435789.1(MAGEB17-AS1):n.794-374T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.64 ( 16237 hom., 20551 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

MAGEB17-AS1
ENST00000435789.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Variant links:

Genes affected

MAGEB17-AS1 (HGNC:56739): (MAGEB17 antisense RNA 1)

MAGEB17-AS1 links:

LOC128966703 (HGNC:):

LOC128966703 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC128966703	XR_008485585.1 linkuse as main transcript	n.1707-374T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MAGEB17-AS1	ENST00000435789.1 linkuse as main transcript	n.794-374T>G	intron_variant, non_coding_transcript_variant	5
MAGEB17-AS1	ENST00000422438.5 linkuse as main transcript	n.161-374T>G	intron_variant, non_coding_transcript_variant	3
MAGEB17-AS1	ENST00000454712.7 linkuse as main transcript	n.631-374T>G	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

70234

AN:

110365

Hom.:

16234

Cov.:

AF XY:

0.628

AC XY:

20498

AN XY:

32631

show subpopulations

Gnomad AFR

AF:

0.778

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.630

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.547

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.613

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.636

AC:

70279

AN:

110418

Hom.:

16237

Cov.:

AF XY:

0.629

AC XY:

20551

AN XY:

32694

show subpopulations

Gnomad4 AFR

AF:

0.778

Gnomad4 AMR

AF:

0.629

Gnomad4 ASJ

AF:

0.544

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.565

Gnomad4 FIN

AF:

0.547

Gnomad4 NFE

AF:

0.573

Gnomad4 OTH

AF:

0.612

Alfa

AF:

0.568

Hom.:

34127

Bravo

AF:

0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.83

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