16-84544635-A-G

Variant names:

• chr16-84544635-A-G
• rs371915
• ENST00000926571.1:c.-26+9311T>C

Variant summary

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

The ENST00000565079.5(MEAK7):​c.-26+9311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,206 control chromosomes in the GnomAD database, including 54,908 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 0.85 (54908 hom., cov: 34)
• Consequence: MEAK7 ENST00000565079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 17 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565079.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEAK7	ENST00000926571.1		c.-26+9311T>C		intron	N/A	ENSP00000596630.1
	MEAK7	ENST00000565079.5	TSL:4	c.-26+9311T>C		intron	N/A	ENSP00000457557.1	H3BUB0

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129134 AN: 152088 Hom.: 54870 Cov.: 34

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.849 AC: 129229 AN: 152206 Hom.: 54908 Cov.: 34 AF XY: 0.847 AC XY: 63020 AN XY: 74402

African (AFR) AF: 0.822 AC: 34119 AN: 41516

American (AMR) AF: 0.833 AC: 12738 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3470

East Asian (EAS) AF: 0.893 AC: 4614 AN: 5166

South Asian (SAS) AF: 0.768 AC: 3703 AN: 4820

European-Finnish (FIN) AF: 0.842 AC: 8932 AN: 10610

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59157 AN: 68010

Other (OTH) AF: 0.864 AC: 1821 AN: 2108

Alfa AF: 0.864 Hom.: 163593

Bravo AF: 0.851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.090
DANN	Benign	0.084
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs371915; hg19: chr16-84578241;