chr21-22436064-A-G

Variant names:

• chr21-22436064-A-G
• rs6518154

Variant summary

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

The variant allele was found at a frequency of 0.964 in 152,260 control chromosomes in the GnomAD database, including 70,747 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 0.96 (70747 hom., cov: 32)
• Consequence: MAPK6P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 2 publications found

Genes affected

MAPK6P2 (HGNC:16756): (mitogen-activated protein kinase 6 pseudogene 2)

ENSG00000295777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732680.1. 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
	ENSG00000295777	ENST00000732680.1		n.259-33855T>C		intron	N/A
	ENSG00000295777	ENST00000732681.1		n.254-5045T>C		intron	N/A
	ENSG00000295777	ENST00000732682.1		n.209+12770T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.964 AC: 146630 AN: 152144 Hom.: 70688 Cov.: 32

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.954

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

GnomAD4 genome AF: 0.964 AC: 146747 AN: 152260 Hom.: 70747 Cov.: 32 AF XY: 0.965 AC XY: 71846 AN XY: 74442

African (AFR) AF: 0.987 AC: 41015 AN: 41546

American (AMR) AF: 0.970 AC: 14837 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3297 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5163 AN: 5170

South Asian (SAS) AF: 0.948 AC: 4578 AN: 4828

European-Finnish (FIN) AF: 0.963 AC: 10213 AN: 10606

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64461 AN: 68028

Other (OTH) AF: 0.954 AC: 2017 AN: 2114

Alfa AF: 0.956 Hom.: 5815

Bravo AF: 0.966

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.29
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs6518154; hg19: chr21-23808384;