rs7290469

chr22-21796693-G-A

Variant summary

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

The NM_002745.5(MAPK1):c.609+2319C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,654 control chromosomes in the GnomAD database, including 9,553 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 0.34 (9553 hom., cov: 30)
• Consequence: MAPK1 NM_002745.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

MAPK1 (HGNC:6871): (mitogen-activated protein kinase 1) This gene encodes a member of the MAP kinase family. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. The activation of this kinase requires its phosphorylation by upstream kinases. Upon activation, this kinase translocates to the nucleus of the stimulated cells, where it phosphorylates nuclear targets. One study also suggests that this protein acts as a transcriptional repressor independent of its kinase activity. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. Two alternatively spliced transcript variants encoding the same protein, but differing in the UTRs, have been reported for this gene. [provided by RefSeq, Jan 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPK1	NM_002745.5	c.609+2319C>T		intron_variant		ENST00000215832.11
MAPK1	NM_138957.3	c.609+2319C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPK1	ENST00000215832.11	c.609+2319C>T		intron_variant		1	NM_002745.5	P1
MAPK1	ENST00000398822.7	c.609+2319C>T		intron_variant		1		P1
MAPK1	ENST00000544786.1	c.609+2319C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 51939 AN: 151536 Hom.: 9561 Cov.: 30

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.343 AC: 51951 AN: 151654 Hom.: 9553 Cov.: 30 AF XY: 0.337 AC XY: 24992 AN XY: 74140

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.402

Alfa AF: 0.414 Hom.: 26743

Bravo AF: 0.342

Asia WGS AF: 0.254 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.35
Dann	Benign	0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7290469; hg19: chr22-22150982;