7-79453799-C-CGT

Position:

• chr7-79453799-C-CGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The ENST00000426835.6(MAGI2-AS3):​n.189+631_189+632dupGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 163,866 control chromosomes in the GnomAD database, including 41 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.019 (41 hom., cov: 31)
  • Exomes 𝑓: 0.00055 (0 hom.)
• Consequence: MAGI2-AS3 ENST00000426835.6 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.25

Genes affected

MAGI2-AS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-79453799-C-CGT is Benign according to our data. Variant chr7-79453799-C-CGT is described in ClinVar as [Likely_benign]. Clinvar id is 1316503.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0193 (2853/147604) while in subpopulation AFR AF= 0.0431 (1748/40544). AF 95% confidence interval is 0.0414. There are 41 homozygotes in gnomad4. There are 1426 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 41 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGI2-AS3	NR_038345.1	n.235+631_235+632dupGT		intron_variant
MAGI2-AS3	NR_038346.1	n.304+167_304+168dupGT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGI2-AS3	ENST00000426835.6	n.189+631_189+632dupGT		intron_variant		3
MAGI2-AS3	ENST00000429408.6	n.310+631_310+632dupGT		intron_variant		3
MAGI2-AS3	ENST00000446159.6	n.103+167_103+168dupGT		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0192 AC: 2836 AN: 147546 Hom.: 40 Cov.: 31

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0201

Gnomad AMR AF: 0.0144

Gnomad ASJ AF: 0.00353

Gnomad EAS AF: 0.00993

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.00329

Gnomad MID AF: 0.0200

Gnomad NFE AF: 0.00947

Gnomad OTH AF: 0.0147

GnomAD4 exome AF: 0.000553 AC: 9 AN: 16262 Hom.: 0 Cov.: 0 AF XY: 0.000810 AC XY: 7 AN XY: 8638

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00142

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000619

Gnomad4 OTH exome AF: 0.00100

GnomAD4 genome AF: 0.0193 AC: 2853 AN: 147604 Hom.: 41 Cov.: 31 AF XY: 0.0198 AC XY: 1426 AN XY: 71984

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.0145

Gnomad4 ASJ AF: 0.00353

Gnomad4 EAS AF: 0.00995

Gnomad4 SAS AF: 0.0248

Gnomad4 FIN AF: 0.00329

Gnomad4 NFE AF: 0.00946

Gnomad4 OTH AF: 0.0150

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 06, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112104600; hg19: chr7-79083115;