Variant chr7-79453831-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NR_038346.1(MAGI2-AS3):n.304+176C>G 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 0.0434 in 153,534 control chromosomes in the GnomAD database, including 448 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.044 ( 448 hom., cov: 32)

Exomes 𝑓: 0.0029 ( 0 hom. )

Consequence

MAGI2-AS3
NR_038346.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.06

Variant links:

Genes affected

MAGI2-AS3 (HGNC:40862): (MAGI2 antisense RNA 3)

MAGI2-AS3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 7-79453831-C-G is Benign according to our data. Variant chr7-79453831-C-G is described in ClinVar as [Benign]. Clinvar id is 1286023.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGI2-AS3	NR_038346.1 linkuse as main transcript	n.304+176C>G		intron_variant, non_coding_transcript_variant
MAGI2-AS3	NR_038345.1 linkuse as main transcript	n.235+640C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGI2-AS3	ENST00000426835.6 linkuse as main transcript	n.189+640C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0438

AC:

6638

AN:

151690

Hom.:

444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0193

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00879

Gnomad SAS

AF:

0.0193

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000515

Gnomad OTH

AF:

0.0253

GnomAD4 exome

AF:

0.00290

AC:

AN:

1726

Hom.:

Cov.:

AF XY:

0.00296

AC XY:

AN XY:

1012

show subpopulations

Gnomad4 AFR exome

AF:

0.0667

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0192

Gnomad4 SAS exome

AF:

0.00943

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0102

GnomAD4 genome

AF:

0.0439

AC:

6661

AN:

151808

Hom.:

448

Cov.:

AF XY:

0.0435

AC XY:

3226

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.0193

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00881

Gnomad4 SAS

AF:

0.0191

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000516

Gnomad4 OTH

AF:

0.0251

Alfa

AF:

0.00694

Hom.:

Bravo

AF:

0.0495

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 02, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.79

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over