chr16-30119172-C-A

Variant names:

• chr16-30119172-C-A
• rs11865086
• NM_002746.3:c.354-634G>T

Variant summary

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

The NM_002746.3(MAPK3):​c.354-634G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 149,156 control chromosomes in the GnomAD database, including 23,626 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 0.55 (23626 hom., cov: 28)
• Consequence: MAPK3 NM_002746.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 41 publications found

Genes affected

MAPK3 (HGNC:6877): (mitogen-activated protein kinase 3) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act in a signaling cascade that regulates various cellular processes such as proliferation, differentiation, and cell cycle progression in response to a variety of extracellular signals. This kinase is activated by upstream kinases, resulting in its translocation to the nucleus where it phosphorylates nuclear targets. Alternatively spliced transcript variants encoding different protein isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPK3	NM_002746.3	c.354-634G>T		intron_variant	Intron 2 of 8	ENST00000263025.9	NP_002737.2
MAPK3	NM_001040056.3	c.354-634G>T		intron_variant	Intron 2 of 6		NP_001035145.1
MAPK3	NM_001109891.2	c.354-634G>T		intron_variant	Intron 2 of 7		NP_001103361.1
MAPK3	XR_243293.2	n.365-634G>T		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPK3	ENST00000263025.9	c.354-634G>T		intron_variant	Intron 2 of 8	1	NM_002746.3	ENSP00000263025.4

Frequencies

GnomAD3 genomes AF: 0.551 AC: 82134 AN: 149064 Hom.: 23596 Cov.: 28

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.551 AC: 82206 AN: 149156 Hom.: 23626 Cov.: 28 AF XY: 0.553 AC XY: 40125 AN XY: 72588

African (AFR) AF: 0.694 AC: 28180 AN: 40600

American (AMR) AF: 0.624 AC: 9368 AN: 15004

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1827 AN: 3452

East Asian (EAS) AF: 0.671 AC: 3416 AN: 5088

South Asian (SAS) AF: 0.564 AC: 2668 AN: 4730

European-Finnish (FIN) AF: 0.460 AC: 4507 AN: 9794

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30578 AN: 67230

Other (OTH) AF: 0.552 AC: 1142 AN: 2068

Alfa AF: 0.488 Hom.: 32357

Bravo AF: 0.574

Asia WGS AF: 0.660 AC: 2243 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.22
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11865086; hg19: chr16-30130493;