rs451480

chr16-84541935-T-Cchr16-84541935-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000565079.5(MEAK7):c.-26+12011A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,188 control chromosomes in the GnomAD database, including 49,534 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 0.79 (49534 hom., cov: 33)
• Consequence: MEAK7 ENST00000565079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

MEAK7 (HGNC:29325): (MTOR associated protein, eak-7 homolog) Involved in several processes, including TOR signaling; positive regulation of protein localization to lysosome; and response to insulin. Located in cytosol; lysosomal membrane; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEAK7	ENST00000565079.5	c.-26+12011A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119661 AN: 152070 Hom.: 49517 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.787 AC: 119716 AN: 152188 Hom.: 49534 Cov.: 33 AF XY: 0.785 AC XY: 58384 AN XY: 74404

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.798

Alfa AF: 0.886 Hom.: 8114

Bravo AF: 0.760

Asia WGS AF: 0.634 AC: 2207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.11
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs451480; hg19: chr16-84575541;