7-79453745-G-T

Position:

• chr7-79453745-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_038346.1(MAGI2-AS3):​n.304+90G>T 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 0.0167 in 213,792 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.020 (74 hom., cov: 33)
  • Exomes 𝑓: 0.0085 (15 hom.)
• Consequence: MAGI2-AS3 NR_038346.1 intron, non_coding_transcript
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.43

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 7-79453745-G-T is Benign according to our data. Variant chr7-79453745-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1317662.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGI2-AS3	NR_038346.1	n.304+90G>T		intron_variant, non_coding_transcript_variant
MAGI2-AS3	NR_038345.1	n.235+554G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGI2-AS3	ENST00000426835.6	n.189+554G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0200 AC: 3036 AN: 151950 Hom.: 74 Cov.: 33

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00623

Gnomad OTH AF: 0.0172

GnomAD4 exome AF: 0.00851 AC: 525 AN: 61728 Hom.: 15 Cov.: 4 AF XY: 0.0110 AC XY: 355 AN XY: 32302

Gnomad4 AFR exome AF: 0.0110

Gnomad4 AMR exome AF: 0.00632

Gnomad4 ASJ exome AF: 0.00930

Gnomad4 EAS exome AF: 0.0415

Gnomad4 SAS exome AF: 0.0369

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00317

Gnomad4 OTH exome AF: 0.0109

GnomAD4 genome AF: 0.0200 AC: 3036 AN: 152064 Hom.: 74 Cov.: 33 AF XY: 0.0208 AC XY: 1548 AN XY: 74328

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0656

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00622

Gnomad4 OTH AF: 0.0175

Alfa AF: 0.00424 Hom.: 2

Bravo AF: 0.0212

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 25, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	17
DANN	Benign	0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs74394893; hg19: chr7-79083061;