16-84503104-T-C

Variant names:

• chr16-84503104-T-C
• rs392747
• NM_020947.4:c.-26+1497A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020947.4(MEAK7):​c.-26+1497A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,210 control chromosomes in the GnomAD database, including 2,458 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 0.17 (2458 hom., cov: 33)
• Consequence: MEAK7 NM_020947.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEAK7	NM_020947.4	c.-26+1497A>G		intron_variant	Intron 1 of 7	ENST00000343629.11	NP_065998.3
MEAK7	XM_005256075.3	c.-26+854A>G		intron_variant	Intron 2 of 8		XP_005256132.1
MEAK7	XM_017023511.2	c.-26+1325A>G		intron_variant	Intron 1 of 7		XP_016879000.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEAK7	ENST00000343629.11	c.-26+1497A>G		intron_variant	Intron 1 of 7	1	NM_020947.4	ENSP00000343635.6

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25985 AN: 152092 Hom.: 2461 Cov.: 33

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.171 AC: 25995 AN: 152210 Hom.: 2458 Cov.: 33 AF XY: 0.173 AC XY: 12886 AN XY: 74428

African (AFR) AF: 0.0886 AC: 3681 AN: 41558

American (AMR) AF: 0.162 AC: 2484 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 581 AN: 3472

East Asian (EAS) AF: 0.0891 AC: 462 AN: 5188

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4822

European-Finnish (FIN) AF: 0.213 AC: 2257 AN: 10588

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14652 AN: 67976

Other (OTH) AF: 0.165 AC: 349 AN: 2114

Alfa AF: 0.195 Hom.: 383

Bravo AF: 0.160

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.60
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs392747; hg19: chr16-84536710;