chr16-84541935-T-C

Variant names:

• chr16-84541935-T-C
• rs451480
• ENST00000565079.5:c.-26+12011A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEAK7	ENST00000565079.5	TSL:4	c.-26+12011A>G		intron	N/A	ENSP00000457557.1

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

African (AFR) AF: 0.542 AC: 22472 AN: 41458

American (AMR) AF: 0.784 AC: 11986 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3205 AN: 3472

East Asian (EAS) AF: 0.490 AC: 2538 AN: 5176

South Asian (SAS) AF: 0.795 AC: 3831 AN: 4818

European-Finnish (FIN) AF: 0.926 AC: 9835 AN: 10616

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63102 AN: 68038

Other (OTH) AF: 0.798 AC: 1686 AN: 2112

Alfa AF: 0.883 Hom.: 16428

Bravo AF: 0.760

Asia WGS AF: 0.634 AC: 2207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.60
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs451480; hg19: chr16-84575541;