rs16974016

Variant names:

• chr16-84516364-G-A
• rs16974016
• ENST00000565079.5:c.-25-18253C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-84516364-G-A
• chr16-84516364-G-C

Variant summary

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

The ENST00000565079.5(MEAK7):​c.-25-18253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,164 control chromosomes in the GnomAD database, including 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 0.053 (534 hom., cov: 34)
• Consequence: MEAK7 ENST00000565079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

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]

LOC124903735 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903735	XR_007065148.1	n.981-1803G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEAK7	ENST00000565079.5	c.-25-18253C>T		intron_variant	Intron 1 of 3	4		ENSP00000457557.1

Frequencies

GnomAD3 genomes AF: 0.0527 AC: 8015 AN: 152046 Hom.: 532 Cov.: 34

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0527 AC: 8025 AN: 152164 Hom.: 534 Cov.: 34 AF XY: 0.0606 AC XY: 4504 AN XY: 74360

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0309

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0295

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0316 Hom.: 61

Bravo AF: 0.0528

Asia WGS AF: 0.156 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16974016; hg19: chr16-84549970;