16-84480696-G-GC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_020947.4(MEAK7):c.1089_1090insG(p.Gln364AlafsTer12) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 1,612,464 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00015 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00012 (1 hom.)
• Consequence: MEAK7 NM_020947.4 frameshift
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.41

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 16-84480696-G-GC is Benign according to our data. Variant chr16-84480696-G-GC is described in ClinVar as [Likely_benign]. Clinvar id is 742235.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEAK7	NM_020947.4	c.1089_1090insG	p.Gln364AlafsTer12	frameshift_variant	7/8	ENST00000343629.11
MEAK7	XM_005256075.3	c.1089_1090insG	p.Gln364AlafsTer12	frameshift_variant	8/9
MEAK7	XM_017023511.2	c.1089_1090insG	p.Gln364AlafsTer12	frameshift_variant	7/8
MEAK7	XM_047434410.1	c.1089_1090insG	p.Gln364AlafsTer12	frameshift_variant	7/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEAK7	ENST00000343629.11	c.1089_1090insG	p.Gln364AlafsTer12	frameshift_variant	7/8	1	NM_020947.4	P1
MEAK7	ENST00000566995.5	c.*503_*504insG		3_prime_UTR_variant, NMD_transcript_variant	8/9	5
MEAK7	ENST00000570036.5	c.*1144_*1145insG		3_prime_UTR_variant, NMD_transcript_variant	8/9	2

Frequencies

GnomAD3 genomes AF: 0.000151 AC: 23 AN: 152022 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.000480

GnomAD4 exome AF: 0.000125 AC: 182 AN: 1460324 Hom.: 1 Cov.: 30 AF XY: 0.000124 AC XY: 90 AN XY: 726460

Gnomad4 AFR exome AF: 0.0000897

Gnomad4 AMR exome AF: 0.0000673

Gnomad4 ASJ exome AF: 0.0000384

Gnomad4 EAS exome AF: 0.000959

Gnomad4 SAS exome AF: 0.0000930

Gnomad4 FIN exome AF: 0.000113

Gnomad4 NFE exome AF: 0.000108

Gnomad4 OTH exome AF: 0.0000497

GnomAD4 genome AF: 0.000151 AC: 23 AN: 152140 Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11 AN XY: 74390

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.000475

Bravo AF: 0.000159

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

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs549073767; hg19: chr16-84514302;