rs6518154

Variant names:

• chr21-22436064-A-G
• rs6518154

Your query was ambiguous. Multiple possible variants found:

• chr21-22436064-A-G
• chr21-22436064-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPK6P2		n.22436064A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295777	ENST00000732680.1	n.259-33855T>C		intron_variant	Intron 1 of 1
ENSG00000295777	ENST00000732681.1	n.254-5045T>C		intron_variant	Intron 1 of 2
ENSG00000295777	ENST00000732682.1	n.209+12770T>C		intron_variant	Intron 2 of 3

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 v4.3

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;